Many thanks to those of you who have submitted details of new or missing enzymes, or updates to existing enzymes.
An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating)
Reaction: UDP-glucuronate + NAD+ = UDP-β-L-threo-pentapyranos-4-ulose + CO2 + NADH + H+
Other name(s): UDP-GlcUA decarboxylase; ArnADH
Systematic name: UDP-glucuronate:NAD+ oxidoreductase (decarboxylating)
Comments: The activity is part of a bifunctional enzyme also performing the reaction of EC 2.1.2.13 (UDP-4-amino-4-deoxy-L-arabinose formyltransferase).
References:
1. Breazeale, S.D., Ribeiro, A.A., McClerren, A.L. and Raetz, C.R.H. A formyltransferase required for polymyxin resistance in Escherichia coli and the modification of lipid A with 4-amino-4-deoxy-L-arabinose. Identification and function of UDP-4-deoxy-4-formamido-L-arabinose. J. Biol. Chem. 280 (2005) 14154-14167. [PMID: 15695810]
2. Gatzeva-Topalova, P.Z., May, A.P. and Sousa, M.C. Crystal structure of Escherichia coli ArnA (PmrI) decarboxylase domain. A key enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance. Biochemistry 43 (2004) 13370-13379. [PMID: 15491143]
3. Williams, G.J., Breazeale, S.D., Raetz, C.R.H. and Naismith, J.H. Structure and function of both domains of ArnA, a dual function decarboxylase and a formyltransferase, involved in 4-amino-4-deoxy-L-arabinose biosynthesis. J. Biol. Chem. 280 (2005) 23000-23008. [PMID: 15809294]
4. Gatzeva-Topalova, P.Z., May, A.P. and Sousa, M.C. Structure and mechanism of ArnA: conformational change implies ordered dehydrogenase mechanism in key enzyme for polymyxin resistance. Structure 13 (2005) 929-942. [PMID: 15939024]
5. Yan, A., Guan, Z. and Raetz, C.R.H. An undecaprenyl phosphate-aminoarabinose flippase required for polymyxin resistance in Escherichia coli. J. Biol. Chem. 282 (2007) 36077-36089. [PMID: 17928292]
Accepted name: S-(hydroxymethyl)mycothiol dehydrogenase
Reaction: S-(hydroxymethyl)mycothiol + NAD+ = S-formylmycothiol + NADH + H+
Glossary: mycothiol = 1-O-[2-(N-acetyl-L-cysteinamido)-2-deoxy-α-D-glucopyranosyl]-D-myo-inositol
Other name(s): NAD/factor-dependent formaldehyde dehydrogenase; mycothiol-dependent formaldehyde dehydrogenase
Systematic name: S-(hydroxymethyl)mycothiol:NAD+ oxidoreductase
Comments: S-hydroxymethylmycothiol is believed to form spontaneously from formaldehyde and mycothiol. This enzyme oxidizes the product of this spontaneous reaction to S-formylmycothiol, in a reaction that is analogous to EC 1.1.1.284, S-(hydroxymethyl)glutathione dehydrogenase.
References:
1. Misset-Smits, M., Van Ophem, P.W., Sakuda, S. and Duine, J.A. Mycothiol, 1-O-(2'-[N-acetyl-L-cysteinyl]amido-2'-deoxy-α-D-glucopyranosyl)-D-myo-inositol, is the factor of NAD/factor-dependent formaldehyde dehydrogenase. FEBS Lett. 409 (1997) 221-222. [PMID: 9202149]
2. Norin, A., Van Ophem, P.W., Piersma, S.R., Person, B., Duine, J.A. and Jornvall, H. Mycothiol-dependent formaldehyde dehydrogenase, a prokaryotic medium-chain dehydrogenase/reductase, phylogenetically links different eukaryotic alcohol dehydrogenase's - primary structure, conformational modelling and functional correlations. Eur. J. Biochem. 248 (1997) 282-289. [PMID: 9346279]
3. Vogt, R.N., Steenkamp, D.J., Zheng, R. and Blanchard, J.S. The metabolism of nitrosothiols in the Mycobacteria: identification and characterization of S-nitrosomycothiol reductase. Biochem. J. 374 (2003) 657-666. [PMID: 12809551]
4. Rawat, M. and Av-Gay, Y. Mycothiol-dependent proteins in actinomycetes. FEMS Microbiol. Rev. 31 (2007) 278-292. [PMID: 17286835]
Accepted name: polyvinyl alcohol dehydrogenase (cytochrome)
Reaction: polyvinyl alcohol + ferricytochrome c = oxidized polyvinyl alcohol + ferrocytochrome c + H+
Other name(s): PVA dehydrogenase; PVADH
Systematic name: polyvinyl alcohol:ferricytochrome-c oxidoreductase
Comments: A quinoprotein. The enzyme is involved in bacterial polyvinyl alcohol degradation. Some Gram-negative bacteria degrade polyvinyl alcohol by importing it into the periplasmic space, where it is oxidized by polyvinyl alcohol dehydrogenase, an enzyme that is coupled to the respiratory chain via cytochrome c. The enzyme contains a pyrroloquinoline quinone cofactor.
References:
1. Shimao, M., Ninomiya, K., Kuno, O., Kato, N. and Sakazawa, C. Existence of a novel enzyme, pyrroloquinoline quinone-dependent polyvinyl alcohol dehydrogenase, in a bacterial symbiont, Pseudomonas sp. strain VM15C. Appl. Environ. Microbiol. 51 (1986) 268. [PMID: 3513704]
2. Shimao, M., Onishi, S., Kato, N. and Sakazawa, C. Pyrroloquinoline quinone-dependent cytochrome reduction in polyvinyl alcohol-degrading Pseudomonas sp strain VM15C. Appl. Environ. Microbiol. 55 (1989) 275-278. [PMID: 16347841]
3. Mamoto, R., Hu, X., Chiue, H., Fujioka, Y. and Kawai, F. Cloning and expression of soluble cytochrome c and its role in polyvinyl alcohol degradation by polyvinyl alcohol-utilizing Sphingopyxis sp. strain 113P3. J. Biosci. Bioeng. 105 (2008) 147-151. [PMID: 18343342]
4. Hirota-Mamoto, R., Nagai, R., Tachibana, S., Yasuda, M., Tani, A., Kimbara, K. and Kawai, F. Cloning and expression of the gene for periplasmic poly(vinyl alcohol) dehydrogenase from Sphingomonas sp. strain 113P3, a novel-type quinohaemoprotein alcohol dehydrogenase. Microbiology 152 (2006) 1941-1949. [PMID: 16804170]
5. Hu, X., Mamoto, R., Fujioka, Y., Tani, A., Kimbara, K. and Kawai, F. The pva operon is located on the megaplasmid of Sphingopyxis sp. strain 113P3 and is constitutively expressed, although expression is enhanced by PVA. Appl. Microbiol. Biotechnol. 78 (2008) 685-693. [PMID: 18214469]
6. Kawai, F. and Hu, X. Biochemistry of microbial polyvinyl alcohol degradation. Appl. Microbiol. Biotechnol. 84 (2009) 227-237. [PMID: 19590867]
Accepted name: methanol dehydrogenase (cytochrome c)
Reaction: a primary alcohol + 2 cytochrome cL = an aldehyde + 2 reduced cytochrome cL
Other name(s): methanol dehydrogenase; MDH
Systematic name: methanol:cytochrome c oxidoreductase
Comments: A periplasmic quinoprotein alcohol dehydrogenase that only occurs in methylotrophic bacteria. It uses the novel specific cytochrome cL as acceptor. Acts on a wide range of primary alcohols, including ethanol, duodecanol, chloroethanol, cinnamyl alcohol, and also formaldehyde. Activity is stimulated by ammonia or methylamine. It is usually assayed with phenazine methosulphate. Like all other quinoprotein alcohol dehydrogenases it has an 8-bladed 'propeller' structure, a calcium ion bound to the PQQ in the active site and an unusual disulphide ring structure in close proximity to the PQQ. It differs from EC 1.1.2.8, alcohol dehydrogenase (cytochrome c), in having a high affinity for methanol and in having a second essential small subunit (no known function).
References:
1. Anthony, C. and Zatman, L.J. The microbial oxidation of methanol. 2. The methanol-oxidizing enzyme of Pseudomonas sp. M 27. Biochem. J. 92 (1964) 614-621. [PMID: 4378696]
2. Anthony, C. and Zatman, L.J. The microbial oxidation of methanol. The prosthetic group of the alcohol dehydrogenase of Pseudomonas sp. M27: a new oxidoreductase prosthetic group. Biochem. J. 104 (1967) 960-969. [PMID: 6049934]
3. Duine, J.A., Frank, J. and Verweil, P.E.J. Structure and activity of the prosthetic group of methanol dehydrogenase. Eur. J. Biochem. 108 (1980) 187-192. [PMID: 6250827]
4. Salisbury, S.A., Forrest, H.S., Cruse, W.B.T. and Kennard, O. A novel coenzyme from bacterial primary alcohol dehydrogenases. Nature (Lond.) 280 (1979) 843-844. [PMID: 471057]
5. Cox, J.M., Day, D.J. and Anthony, C. The interaction of methanol dehydrogenase and its electron acceptor, cytochrome cL in methylotrophic bacteria . Biochim. Biophys. Acta 1119 (1992) 97-106. [PMID: 1311606]
6. Blake, C.C., Ghosh, M., Harlos, K., Avezoux, A. and Anthony, C. The active site of methanol dehydrogenase contains a disulphide bridge between adjacent cysteine residues. Nat. Struct. Biol. 1 (1994) 102-105. [PMID: 7656012]
7. Xia, Z.X., He, Y.N., Dai, W.W., White, S.A., Boyd, G.D. and Mathews, F.S. Detailed active site configuration of a new crystal form of methanol dehydrogenase from Methylophilus W3A1 at 1.9 Å resolution. Biochemistry 38 (1999) 1214-1220. [PMID: 9930981]
8. Afolabi, P.R., Mohammed, F., Amaratunga, K., Majekodunmi, O., Dales, S.L., Gill, R., Thompson, D., Cooper, J.B., Wood, S.P., Goodwin, P.M. and Anthony, C. Site-directed mutagenesis and X-ray crystallography of the PQQ-containing quinoprotein methanol dehydrogenase and its electron acceptor, cytochrome c(L). Biochemistry 40 (2001) 9799-9809. [PMID: 11502173]
9. Anthony, C. and Williams, P. The structure and mechanism of methanol dehydrogenase. Biochim. Biophys. Acta 1647 (2003) 18-23. [PMID: 12686102]
10. Williams, P.A., Coates, L., Mohammed, F., Gill, R., Erskine, P.T., Coker, A., Wood, S.P., Anthony, C. and Cooper, J.B. The atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens. Acta Crystallogr. D Biol. Crystallogr. 61 (2005) 75-79. [PMID: 15608378]
Accepted name: alcohol dehydrogenase (cytochrome c)
Reaction: a primary alcohol + 2 cytochrome c = an aldehyde + 2 reduced cytochrome c
Other name(s): type I quinoprotein alcohol dehydrogenase; quinoprotein ethanol dehydrogenase
Systematic name: alcohol:cytochrome c oxidoreductase
Comments: A periplasmic PQQ-containing quinoprotein. Occurs in Pseudomonas and Rhodopseudomonas. The enzyme from Pseudomonas aeruginosa uses a specific inducible cytochrome c550 as electron acceptor. Acts on a wide range of primary and secondary alcohols, but not methanol. It has a homodimeric structure [contrasting with the heterotetrameric structure of EC 1.1.2.7, methanol dehydrogenase (cytochrome c)]. It is routinely assayed with phenazine methosulphate as electron acceptor. Activity is stimulated by ammonia or amines. Like all other quinoprotein alcohol dehydrogenases it has an 8-bladed 'propeller' structure, a calcium ion bound to the PQQ in the active site and an unusual disulphide ring structure in close proximity to the PQQ.
References:
1. Rupp, M. and Gorisch, H. Purification, crystallisation and characterization of quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa. Biol. Chem. Hoppe-Seyler 369 (1988) 431-439. [PMID: 3144289]
2. Toyama, H., Fujii, A., Matsushita, K., Shinagawa, E., Ameyama, M. and Adachi, O. Three distinct quinoprotein alcohol dehydrogenases are expressed when Pseudomonas putida is grown on different alcohols. J. Bacteriol. 177 (1995) 2442-2450. [PMID: 7730276]
3. Schobert, M. and Gorisch, H. Cytochrome c550 is an essential component of the quinoprotein ethanol oxidation system in Pseudomonas aeruginosa: cloning and sequencing of the genes encoding cytochrome c550 and an adjacent acetaldehyde dehydrogenase. Microbiology 145 (1999) 471-481. [PMID: 10075429]
4. Keitel, T., Diehl, A., Knaute, T., Stezowski, J.J., Hohne, W. and Gorisch, H. X-ray structure of the quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa: basis of substrate specificity. J. Mol. Biol. 297 (2000) 961-974. [PMID: 10736230]
5. Kay, C.W., Mennenga, B., Gorisch, H. and Bittl, R. Characterisation of the PQQ cofactor radical in quinoprotein ethanol dehydrogenase of Pseudomonas aeruginosa by electron paramagnetic resonance spectroscopy. FEBS Lett. 564 (2004) 69-72. [PMID: 15094044]
6. Mennenga, B., Kay, C.W. and Gorisch, H. Quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa: the unusual disulfide ring formed by adjacent cysteine residues is essential for efficient electron transfer to cytochrome c550. Arch. Microbiol. 191 (2009) 361-367. [PMID: 19224199]
Accepted name: quinoprotein glucose dehydrogenase
Reaction: D-glucose + ubiquinone = D-glucono-1,5-lactone + ubiquinol
Other name(s): membrane-bound glucose dehydrogenase; mGDH; glucose dehydrogenase (PQQ-dependent); glucose dehydrogenase (pyrroloquinoline-quinone); quinoprotein D-glucose dehydrogenase
Systematic name: D-glucose:ubiquinone oxidoreductase
Comments: Integral membrane protein containing PQQ as prosthetic group. It also contains bound ubiquinone and Mg2+ or Ca2+. Electron acceptor is membrane ubiquinone but usually assayed with phenazine methosulfate. Like in all other quinoprotein alcohol dehydrogenases the catalytic domain has an 8-bladed 'propeller' structure. It occurs in a wide range of bacteria. Catalyses a direct oxidation of the pyranose form of D-glucose to the lactone and thence to D-gluconate in the periplasm. Oxidizes other monosaccharides including the pyranose forms of pentoses.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 81669-60-5
References:
1. Yamada, M., Sumi, K., Matsushita, K., Adachi, O. and Yamada, Y. Topological analysis of quinoprotein glucose-dehydrogenase in Escherichia coli and its ubiquinone-binding site. J. Biol. Chem. 268 (1993) 12812-12817. [PMID: 8509415]
2. Dewanti, A.R. and Duine, J.A. Reconstitution of membrane-integrated quinoprotein glucose dehydrogenase apoenzyme with PQQ and the holoenzyme's mechanism of action. Biochemistry 37 (1998) 6810-6818. [PMID: 9578566]
3. Duine, J.A., Frank, J. and Van Zeeland, J.K. Glucose dehydrogenase from Acinetobacter calcoaceticus: a 'quinoprotein'. FEBS Lett. 108 (1979) 443-446. [PMID: 520586]
4. Ameyama, M., Matsushita, K., Ohno, Y., Shinagawa, E. and Adachi, O. Existence of a novel prosthetic group, PQQ, in membrane-bound, electron transport chain-linked, primary dehydrogenases of oxidative bacteria. FEBS Lett. 130 (1981) 179-183. [PMID: 6793395]
5. Cozier, G.E. and Anthony, C. Structure of the quinoprotein glucose dehydrogenase of Escherichia coli modelled on that of methanol dehydrogenase from Methylobacterium extorquens. Biochem. J. 312 (1995) 679-685. [PMID: 8554505]
6. Cozier, G.E., Salleh, R.A. and Anthony, C. Characterization of the membrane quinoprotein glucose dehydrogenase from Escherichia coli and characterization of a site-directed mutant in which histidine-262 has been changed to tyrosine. Biochem. J. 340 (1999) 639-647. [PMID: 10359647]
7. Elias, M.D., Tanaka, M., Sakai, M., Toyama, H., Matsushita, K., Adachi, O. and Yamada, M. C-terminal periplasmic domain of Escherichia coli quinoprotein glucose dehydrogenase transfers electrons to ubiquinone. J. Biol. Chem. 276 (2001) 48356-48361. [PMID: 11604400]
8. James, P.L. and Anthony, C. The metal ion in the active site of the membrane glucose dehydrogenase of Escherichia coli. Biochim. Biophys. Acta 1647 (2003) 200-205. [PMID: 12686133]
9. Elias, M.D., Nakamura, S., Migita, C.T., Miyoshi, H., Toyama, H., Matsushita, K., Adachi, O. and Yamada, M. Occurrence of a bound ubiquinone and its function in Escherichia coli membrane-bound quinoprotein glucose dehydrogenase. J. Biol. Chem. 279 (2004) 3078-3083. [PMID: 14612441]
10. Mustafa, G., Ishikawa, Y., Kobayashi, K., Migita, C.T., Elias, M.D., Nakamura, S., Tagawa, S. and Yamada, M. Amino acid residues interacting with both the bound quinone and coenzyme, pyrroloquinoline quinone, in Escherichia coli membrane-bound glucose dehydrogenase. J. Biol. Chem. 283 (2008) 22215-22221. [PMID: 18550551]
Accepted name: alcohol dehydrogenase (quinone)
Reaction: ethanol + ubiquinone = acetaldehyde + ubiquinol
Other name(s): type III ADH; membrane associated quinohemoprotein alcohol dehydrogenase
Systematic name: alcohol:quinone oxidoreductase
Comments: Only described in acetic acid bacteria where it is involved in acetic acid production. Associated with membrane. Electron acceptor is membrane ubiquinone. A model structure suggests that, like all other quinoprotein alcohol dehydrogenases, the catalytic subunit has an 8-bladed 'propeller' structure, a calcium ion bound to the PQQ in the active site and an unusual disulfide ring structure in close proximity to the PQQ; the catalytic subunit also has a heme c in the C-terminal domain. The enzyme has two additional subunits, one of which contains three molecules of heme c. It does not require amines for activation. It has a restricted substrate specificity, oxidising a few primary alcohols (C2 to C6), but not methanol, secondary alcohols and some aldehydes. It is assayed with phenazine methosulfate or with ferricyanide.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number:
References:
1. Gomez-Manzo, S., Contreras-Zentella, M., Gonzalez-Valdez, A., Sosa-Torres, M., Arreguin-Espinoza, R. and Escamilla-Marvan, E. The PQQ-alcohol dehydrogenase of Gluconacetobacter diazotrophicus. Int. J. Food Microbiol. 125 (2008) 71-78. [PMID: 18321602]
2. Shinagawa, E., Toyama, H., Matsushita, K., Tuitemwong, P., Theeragool, G. and Adachi, O. A novel type of formaldehyde-oxidizing enzyme from the membrane of Acetobacter sp. SKU 14. Biosci. Biotechnol. Biochem. 70 (2006) 850-857. [PMID: 16636451]
3. Chinnawirotpisan, P., Theeragool, G., Limtong, S., Toyama, H., Adachi, O.O. and Matsushita, K. Quinoprotein alcohol dehydrogenase is involved in catabolic acetate production, while NAD-dependent alcohol dehydrogenase in ethanol assimilation in Acetobacter pasteurianus SKU1108. J. Biosci. Bioeng. 96 (2003) 564-571. [PMID: 16233574]
4. Frebortova, J., Matsushita, K., Arata, H. and Adachi, O. Intramolecular electron transport in quinoprotein alcohol dehydrogenase of Acetobacter methanolicus: a redox-titration stud. Biochim. Biophys. Acta 1363 (1998) 24-34. [PMID: 9526036]
5. Matsushita, K., Kobayashi, Y., Mizuguchi, M., Toyama, H., Adachi, O., Sakamoto, K. and Miyoshi, H. A tightly bound quinone functions in the ubiquinone reaction sites of quinoprotein alcohol dehydrogenase of an acetic acid bacterium, Gluconobacter suboxydans. Biosci. Biotechnol. Biochem. 72 (2008) 2723-2731. [PMID: 18838797]
6. Matsushita, K., Yakushi, T., Toyama, H., Shinagawa, E. and Adachi, O. Function of multiple heme c moieties in intramolecular electron transport and ubiquinone reduction in the quinohemoprotein alcohol dehydrogenase-cytochrome c complex of Gluconobacter suboxydans. J. Biol. Chem. 271 (1996) 4850-4857. [PMID: 8617755]
7. Matsushita, K., Takaki, Y., Shinagawa, E., Ameyama, M. and Adachi, O. Ethanol oxidase respiratory chain of acetic acid bacteria. Reactivity with ubiquinone of pyrroloquinoline quinone-dependent alcohol dehydrogenases purified from Acetobacter aceti and Gluconobacter suboxydans. Biosci. Biotechnol. Biochem. 56 (1992) 304-310.
8. Matsushita, K., Toyama, H. and Adachi, O. Respiratory chains and bioenergetics of acetic acid bacteria. Adv. Microb. Physiol. 36 (1994) 247-301. [PMID: 7942316]
9. Cozier, G.E., Giles, I.G. and Anthony, C. The structure of the quinoprotein alcohol dehydrogenase of Acetobacter aceti modelled on that of methanol dehydrogenase from Methylobacterium extorquens. Biochem. J. 308 (1995) 375-379. [PMID: 7772016]
EC 1.1.98 With other, known, acceptors
Accepted name: alcohol dehydrogenase (azurin)
Reaction: a primary alcohol + azurin = an aldehyde + reduced azurin
Other name(s): type II quinoprotein alcohol dehydrogenase; quinohaemoprotein ethanol dehydrogenase; QHEDH; ADHIIB
Systematic name: alcohol:azurin oxidoreductase
Comments: A soluble, periplasmic PQQ-containing quinohemoprotein. Also contains a single heme c. Occurs in Comamonas and Pseudomonas. Does not require an amine activator. Oxidizes a wide range of primary and secondary alcohols, and also aldehydes and large substrates such as sterols; methanol is not a substrate. Usually assayed with phenazine methosulphate or ferricyanide. Like all other quinoprotein alcohol dehydrogenases it has an 8-bladed 'propeller' structure, a calcium ion bound to the PQQ in the active site and an unusual disulphide ring structure in close proximity to the PQQ.
References:
1. Groen, B.W., van Kleef, M.A. and Duine, J.A. Quinohaemoprotein alcohol dehydrogenase apoenzyme from Pseudomonas testosteroni. Biochem. J. 234 (1986) 611-615. [PMID: 3521592]
2. de Jong, G.A., Caldeira, J., Sun, J., Jongejan, J.A., de Vries, S., Loehr, T.M., Moura, I., Moura, J.J. and Duine, J.A. Characterization of the interaction between PQQ and heme c in the quinohemoprotein ethanol dehydrogenase from Comamonas testosteroni. Biochemistry 34 (1995) 9451-9458. [PMID: 7626615]
3. Toyama, H., Fujii, A., Matsushita, K., Shinagawa, E., Ameyama, M. and Adachi, O. Three distinct quinoprotein alcohol dehydrogenases are expressed when Pseudomonas putida is grown on different alcohols. J. Bacteriol. 177 (1995) 2442-2450. [PMID: 7730276]
4. Matsushita, K., Yamashita, T., Aoki, N., Toyama, H. and Adachi, O. Electron transfer from quinohemoprotein alcohol dehydrogenase to blue copper protein azurin in the alcohol oxidase respiratory chain of Pseudomonas putida HK5. Biochemistry 38 (1999) 6111-6118. [PMID: 10320337]
5. Chen, Z.W., Matsushita, K., Yamashita, T., Fujii, T.A., Toyama, H., Adachi, O., Bellamy, H.D. and Mathews, F.S. Structure at 1.9 Å resolution of a quinohemoprotein alcohol dehydrogenase from Pseudomonas putida HK5. Structure 10 (2002) 837-849. [PMID: 12057198]
6. Oubrie, A., Rozeboom, H.J., Kalk, K.H., Huizinga, E.G. and Dijkstra, B.W. Crystal structure of quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni: structural basis for substrate oxidation and electron transfer. J. Biol. Chem. 277 (2002) 3727-3732. [PMID: 11714714]
[EC 1.1.99.8 Transferred entry: alcohol dehydrogenase (acceptor). Now EC 1.1.2.7, methanol dehydrogenase (cytochrome c) and EC 1.1.2.8, alcohol dehydrogenase (cytochrome c). (EC 1.1.99.8 created 1972, modified 1982, deleted 2010)]
[EC 1.1.99.23 Transferred entry: polyvinyl-alcohol dehydrogenase (acceptor). Now EC 1.1.2.6, polyvinyl alcohol dehydrogenase (cytochrome) (EC 1.1.99.23 created 1989, deleted 2010)]
Accepted name: glucose-6-phosphate dehydrogenase (coenzyme-F420)
Reaction: D-glucose 6-phosphate + oxidized coenzyme F420 = D-glucono-1,5-lactone 6-phosphate + reduced coenzyme F420
Other name(s): coenzyme F420-dependent glucose-6-phosphate dehydrogenase; F420-dependent glucose-6-phosphate dehydrogenase; FGD1; Rv0407; F420-dependent glucose-6-phosphate dehydrogenase 1
Systematic name: D-glucose-6-phosphate:F420 1-oxidoreductase
Comments: The enzyme is very specific for D-glucose 6-phosphate. No activity with NAD+, NADP+, flavin adenine dinucleotide and flavin mononucleotide [1].
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number:
References:
1. Purwantini, E. and Daniels, L. Purification of a novel coenzyme F420-dependent glucose-6-phosphate dehydrogenase from Mycobacterium smegmatis. J. Bacteriol. 178 (1996) 2861-2866. [PMID: 8631674]
2. Bashiri, G., Squire, C.J., Baker, E.N. and Moreland, N.J. Expression, purification and crystallization of native and selenomethionine labeled Mycobacterium tuberculosis FGD1 (Rv0407) using a Mycobacterium smegmatis expression system. Protein Expr. Purif. 54 (2007) 38-44. [PMID: 17376702]
3. Purwantini, E., Gillis, T.P. and Daniels, L. Presence of F420-dependent glucose-6-phosphate dehydrogenase in Mycobacterium and Nocardia species, but absence from Streptomyces and Corynebacterium species and methanogenic Archaea. FEMS Microbiol. Lett. 146 (1997) 129-134. [PMID: 8997717]
Accepted name: soluble quinoprotein glucose dehydrogenase
Reaction: D-glucose + acceptor = D-glucono-1,5-lactone + reduced acceptor
Other name(s): soluble glucose dehydrogenase; sGDH; glucose dehydrogenase (PQQ-dependent)
Systematic name: D-glucose:acceptor oxidoreductase
Comments: Soluble periplasmic enzyme containing PQQ as prosthetic group, bound to a calcium ion. Electron acceptor is not known. It is assayed with Wurster's Blue or phenazine methosulphate. It has negligible sequence or structure similarity to other quinoproteins. It catalyses an exceptionally high rate of oxidation of a wide range of aldose sugars, including D-glucose, galactose, arabinose and xylose, and also the disaccharides lactose, cellobiose and maltose. It has been described only in Acinetobacter calcoaceticus.
References:
1. Geiger, O. and Gorisch, H. Crystalline quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus. Biochemistry 25 (1986) 6043-6048.
2. Dokter, P., Frank, J. and Duine, J.A. Purification and characterization of quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus L.M.D. 79.41. Biochem. J. 239 (1986) 163-167. [PMID: 3800975]
3. Cleton-Jansen, A.M., Goosen, N., Wenzel, T.J. and van de Putte, P. Cloning of the gene encoding quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus: evidence for the presence of a second enzyme. J. Bacteriol. 170 (1988) 2121-2125. [PMID: 2834325]
4. Matsushita, K., Shinagawa, E., Adachi, O. and Ameyama, M. Quinoprotein D-glucose dehydrogenase of the Acinetobacter calcoaceticus respiratory chain: membrane-bound and soluble forms are different molecular species. Biochemistry 28 (1989) 6276-6280. [PMID: 2551369]
5. Oubrie, A. and Dijkstra, B.W. Structural requirements of pyrroloquinoline quinone dependent enzymatic reactions. Protein Sci. 9 (2000) 1265-1273. [PMID: 10933491]
6. Matsushita, K., Toyama, H., Ameyama, M., Adachi, O., Dewanti, A. and Duine, J.A. Soluble and membrane-bound quinoprotein D-glucose dehydrogenases of the Acinetobacter calcoaceticus: The binding process of PQQ to the apoenzymes. Biosci. Biotechnol. Biochem 59 (1995) 1548-1555.
[EC 1.2.1.66 Transferred entry: mycothiol-dependent formaldehyde dehydrogenase. Now EC 1.1.1.306, S-(hydroxymethyl)mycothiol dehydrogenase (EC 1.2.1.66 created 2000, deleted 2010)]
EC 1.2.5 With a quinone or similar compound as acceptor
Accepted name: pyruvate dehydrogenase (quinone)
Reaction: pyruvate + ubiquinone + H2O = acetate + CO2 + ubiquinol
Other name(s): pyruvate dehydrogenase; pyruvic dehydrogenase; pyruvic (cytochrome b1) dehydrogenase; pyruvate:ubiquinone-8-oxidoreductase; pyruvate oxidase (ambiguous); pyruvate dehydrogenase (cytochrome) (incorrect)
Systematic name: pyruvate:ubiquinone oxidoreductase
Comments: Flavoprotein (FAD) [1]. This bacterial enzyme is located on the inner surface of the cytoplasmic membrane and coupled to the respiratory chain via ubiquinone [2,3]. Does not accept menaquinone. Activity is greatly enhanced by lipids [4,5,6]. Requires thiamine diphosphate [7]. The enzyme can also form acetoin [8].
References:
1. Recny, M.A. and Hager, L.P. Reconstitution of native Escherichia coli pyruvate oxidase from apoenzyme monomers and FAD. J. Biol. Chem. 257 (1982) 12878-12886. [PMID: 6752142]
2. Cunningham, C.C. and Hager, L.P. Reactivation of the lipid-depleted pyruvate oxidase system from Escherichia coli with cell envelope neutral lipids. J. Biol. Chem. 250 (1975) 7139-7146. [PMID: 1100621]
3. Koland, J.G., Miller, M.J. and Gennis, R.B. Reconstitution of the membrane-bound, ubiquinone-dependent pyruvate oxidase respiratory chain of Escherichia coli with the cytochrome d terminal oxidase. Biochemistry 23 (1984) 445-453. [PMID: 6367818]
4. Grabau, C. and Cronan, J.E., Jr. In vivo function of Escherichia coli pyruvate oxidase specifically requires a functional lipid binding site. Biochemistry 25 (1986) 3748-3751. [PMID: 3527254]
5. Wang, A.Y., Chang, Y.Y. and Cronan, J.E., Jr. Role of the tetrameric structure of Escherichia coli pyruvate oxidase in enzyme activation and lipid binding. J. Biol. Chem. 266 (1991) 10959-10966. [PMID: 2040613]
6. Chang, Y.Y. and Cronan, J.E., Jr. Sulfhydryl chemistry detects three conformations of the lipid binding region of Escherichia coli pyruvate oxidase. Biochemistry 36 (1997) 11564-11573. [PMID: 9305946]
7. O'Brien, T.A., Schrock, H.L., Russell, P., Blake, R., 2nd and Gennis, R.B. Preparation of Escherichia coli pyruvate oxidase utilizing a thiamine pyrophosphate affinity column. Biochim. Biophys. Acta 452 (1976) 13-29. [PMID: 791368]
8. Bertagnolli, B.L. and Hager, L.P. Role of flavin in acetoin production by two bacterial pyruvate oxidases. Arch. Biochem. Biophys. 300 (1993) 364-371. [PMID: 8424670]
Accepted name: protoporphyrinogen IX dehydrogenase (menaquinone)
Reaction: protoporphyrinogen IX + 3 menaquinone = protoporphyrin IX + 3 menaquinol
Other name(s): HemG
Systematic name: protoporphyrinogen IX:menaquinone oxidoreductase
Comments: This enzyme enables Escherichia coli to synthesize heme in both aerobic and anaerobic environments.
References:
1. Boynton, T.O., Daugherty, L.E., Dailey, T.A. and Dailey, H.A. Identification of Escherichia coli HemG as a novel, menadione-dependent flavodoxin with protoporphyrinogen oxidase activity. Biochemistry 48 (2009) 6705-6711. [PMID: 19583219]
Accepted name: ferredoxin:thioredoxin reductase
Reaction: 2 reduced ferredoxin + thioredoxin disulfide = 2 oxidized ferredoxin + thioredoxin + 2 H+
Systematic name: ferredoxin:thioredoxin disulfide oxidoreductase
Comments: The enzyme contains a [4Fe-4S] cluster and internal disulfide. It forms a mixed disulfide with thioredoxin on one side, and docks ferredoxin on the other side, enabling two one-electron transfers. The reduced thioredoxins generated by the enzyme activate the Calvin cycle enzymes EC 3.1.3.11 (fructose-bisphosphatase), EC 3.1.3.37 (sedoheptulose-bisphosphatase) and EC 2.7.1.19 (phosphoribulokinase) as well as other chloroplast enzymes by disulfide reduction.
References:
1. Buchanan, B.B. Regulation of CO2 assimilation in oxygenic photosynthesis: the ferredoxin/thioredoxin system. Perspective on its discovery, present status, and future development. Arch. Biochem. Biophys. 288 (1991) 1-9. [PMID: 1910303]
2. Chow, L.P., Iwadate, H., Yano, K., Kamo, M., Tsugita, A., Gardet-Salvi, L., Stritt-Etter, A.L. and Schurmann, P. Amino acid sequence of spinach ferredoxin:thioredoxin reductase catalytic subunit and identification of thiol groups constituting a redox-active disulfide and a [4Fe-4S] cluster. Eur. J. Biochem. 231 (1995) 149-156. [PMID: 7628465]
3. Staples, C.R., Ameyibor, E., Fu, W., Gardet-Salvi, L., Stritt-Etter, A.L., Schurmann, P., Knaff, D.B. and Johnson, M.K. The function and properties of the iron-sulfur center in spinach ferredoxin: thioredoxin reductase: a new biological role for iron-sulfur clusters. Biochemistry 35 (1996) 11425-11434. [PMID: 8784198]
Accepted name: bromide peroxidase
Reaction: RH + HBr + H2O2 = RBr + 2 H2O
Other name(s): bromoperoxidase; haloperoxidase (ambiguous); eosinophil peroxidase
Systematic name: bromide:hydrogen-peroxide oxidoreductase
Comments: Bromoperoxidases of red and brown marine algae (Rhodophyta and Phaeophyta) contain vanadate. They catalyse the bromination of a range of organic molecules such as sesquiterpenes, forming stable C-Br bonds. Bromoperoxidases also oxidize iodides.
References:
1. De Boer, E., Tromp, M.G.M., Plat, H., Krenn, G.E. and Wever, R Vanadium(v) as an essential element for haloperoxidase activity in marine brown-algae - purification and characterization of a vanadium(V)-containing bromoperoxidase from Laminaria saccharina. Biochim. Biophys. Acta 872 (1986) 104-115.
2. Tromp, M.G., Olafsson, G., Krenn, B.E. and Wever, R. Some structural aspects of vanadium bromoperoxidase from Ascophyllum nodosum. Biochim. Biophys. Acta 1040 (1990) 192-198. [PMID: 2400770]
3. Isupov, M.N., Dalby, A.R., Brindley, A.A., Izumi, Y., Tanabe, T., Murshudov, G.N. and Littlechild, J.A. Crystal structure of dodecameric vanadium-dependent bromoperoxidase from the red algae Corallina officinalis. J. Mol. Biol. 299 (2000) 1035-1049. [PMID: 10843856]
4. Carter-Franklin, J.N. and Butler, A. Vanadium bromoperoxidase-catalyzed biosynthesis of halogenated marine natural products. J. Am. Chem. Soc. 126 (2004) 15060-15066. [PMID: 15548002]
5. Ohshiro, T., Littlechild, J., Garcia-Rodriguez, E., Isupov, M.N., Iida, Y., Kobayashi, T. and Izumi, Y. Modification of halogen specificity of a vanadium-dependent bromoperoxidase. Protein Sci. 13 (2004) 1566-1571. [PMID: 15133166]
Accepted name: 2,5-dihydroxypyridine 5,6-dioxygenase
Reaction: 2,5-dihydroxypyridine + O2 = N-formylmaleamic acid
Other name(s): 2,5-dihydroxypyridine oxygenase; pyridine-2,5-diol dioxygenase; NicX
Systematic name: 2,5-dihydroxypyridine:oxygen 5,6-oxidoreductase
Comments: Requires Fe2+.
Links to other databases: BRENDA, EXPASY, KEGG, UM-BBD, CAS registry number: 9029-57-6
References:
1. Behrman, E.J. and Stanier, R.Y. The bacterial oxidation of nicotinic acid. J. Biol. Chem. 228 (1957) 923-945. [PMID: 13475371]
2. Gauthier, J.J. and Rittenberg, S.C. The metabolism of nicotinic acid. I. Purification and properties of 2,5-dihydroxypyridine oxygenase from Pseudomonas putida N-9. J. Biol. Chem. 246 (1971) 3737-3742. [PMID: 5578917]
3. Gauthier, J.J. and Rittenberg, S.C. The metabolism of nicotinic acid. II. 2,5-Dihydroxypyridine oxidation, product formation, and oxygen 18 incorporation. J. Biol. Chem. 246 (1971) 3743-3748. [PMID: 5578918]
4. Jimenez, J.I., Canales, A., Jimenez-Barbero, J., Ginalski, K., Rychlewski, L., Garcia, J.L. and Diaz, E. Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440. Proc. Natl. Acad. Sci. USA 105 (2008) 11329-11334. [PMID: 18678916]
Accepted name: hypoxia-inducible factor-proline dioxygenase
Reaction: hypoxia-inducible factor-L-proline + 2-oxoglutarate + O2 = hypoxia-inducible factor-trans-4-hydroxy-L-proline + succinate + CO2
Other name(s): HIF hydroxylase
Systematic name: hypoxia-inducible factor-L-proline, 2-oxoglutarate:oxygen oxidoreductase (4-hydroxylating)
Comments: Contains iron, and requires ascorbate. Specifically hydroxylates a proline residue in HIF-α, the α subunit of the transcriptional regulator HIF (hypoxia-inducible factor), which targets HIF for proteasomal destruction. The requirement of oxygen for the hydroxylation reaction enables animals to respond to hypoxia.
References:
1. Jaakkola, P., Mole, D.R., Tian, Y.M., Wilson, M.I., Gielbert, J., Gaskell, S.J., Kriegsheim Av, Hebestreit, H.F., Mukherji, M., Schofield, C.J., Maxwell, P.H., Pugh, C.W. and Ratcliffe, P.J. Targeting of HIF-α to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation. Science 292 (2001) 468-472. [PMID: 11292861]
2. Ivan, M., Kondo, K., Yang, H., Kim, W., Valiando, J., Ohh, M., Salic, A., Asara, J.M., Lane, W.S. and Kaelin , W.G., Jr. HIFα targeted for VHL-mediated destruction by proline hydroxylation: implications for O2 sensing. Science 292 (2001) 464-468. [PMID: 11292862]
3. Bruick, R.K. and McKnight, S.L. A conserved family of prolyl-4-hydroxylases that modify HIF. Science 294 (2001) 1337-1340. [PMID: 11598268]
4. Epstein, A.C., Gleadle, J.M., McNeill, L.A., Hewitson, K.S., O'Rourke, J., Mole, D.R., Mukherji, M., Metzen, E., Wilson, M.I., Dhanda, A., Tian, Y.M., Masson, N., Hamilton, D.L., Jaakkola, P., Barstead, R., Hodgkin, J., Maxwell, P.H., Pugh, C.W., Schofield, C.J. and Ratcliffe, P.J. C. elegans EGL-9 and mammalian homologs define a family of dioxygenases that regulate HIF by prolyl hydroxylation. Cell 107 (2001) 43-54. [PMID: 11595184]
5. Oehme, F., Ellinghaus, P., Kolkhof, P., Smith, T.J., Ramakrishnan, S., Hutter, J., Schramm, M. and Flamme, I. Overexpression of PH-4, a novel putative proline 4-hydroxylase, modulates activity of hypoxia-inducible transcription factors. Biochem. Biophys. Res. Commun. 296 (2002) 343-349. [PMID: 12163023]
6. McNeill, L.A., Hewitson, K.S., Gleadle, J.M., Horsfall, L.E., Oldham, N.J., Maxwell, P.H., Pugh, C.W., Ratcliffe, P.J. and Schofield, C.J. The use of dioxygen by HIF prolyl hydroxylase (PHD1). Bioorg. Med. Chem. Lett. 12 (2002) 1547-1550. [PMID: 12039559]
Accepted name: hypoxia-inducible factor-asparagine dioxygenase
Reaction: hypoxia-inducible factor-L-asparagine + 2-oxoglutarate + O2 = hypoxia-inducible factor-(3S)-3-hydroxy-L-asparagine + succinate + CO2
Other name(s): HIF hydroxylase
Systematic name: hypoxia-inducible factor-L-asparagine, 2-oxoglutarate:oxygen oxidoreductase (4-hydroxylating)
Comments: Contains iron, and requires ascorbate. Catalyses hydroxylation of an asparagine in the C-terminal transcriptional activation domain of HIF-α, the α subunit of the transcriptional regulator HIF (hypoxia-inducible factor), which reduces its interaction with the transcriptional coactivator protein p300. The requirement of oxygen for the hydroxylation reaction enables animals to respond to hypoxia.
References:
1. Mahon, P.C., Hirota, K. and Semenza, G.L. FIH-1: a novel protein that interacts with HIF-1α and VHL to mediate repression of HIF-1 transcriptional activity. Genes Dev. 15 (2001) 2675-2686. [PMID: 11641274]
2. Hewitson, K.S., McNeill, L.A., Riordan, M.V., Tian, Y.M., Bullock, A.N., Welford, R.W., Elkins, J.M., Oldham, N.J., Bhattacharya, S., Gleadle, J.M., Ratcliffe, P.J., Pugh, C.W. and Schofield, C.J. Hypoxia-inducible factor (HIF) asparagine hydroxylase is identical to factor inhibiting HIF (FIH) and is related to the cupin structural family. J. Biol. Chem. 277 (2002) 26351-26355. [PMID: 12042299]
4. Lando, D., Peet, D.J., Whelan, D.A., Gorman, J.J. and Whitelaw, M.L. Asparagine hydroxylation of the HIF transactivation domain a hypoxic switch. Science 295 (2002) 858-861. [PMID: 11823643]
5. Koivunen, P., Hirsila, M., Gunzler, V., Kivirikko, K.I. and Myllyharju, J. Catalytic properties of the asparaginyl hydroxylase (FIH) in the oxygen sensing pathway are distinct from those of its prolyl 4-hydroxylases. J. Biol. Chem. 279 (2004) 9899-9904. [PMID: 14701857]
6. Elkins, J.M., Hewitson, K.S., McNeill, L.A., Seibel, J.F., Schlemminger, I., Pugh, C.W., Ratcliffe, P.J. and Schofield, C.J. Structure of factor-inhibiting hypoxia-inducible factor (HIF) reveals mechanism of oxidative modification of HIF-1 α. J. Biol. Chem. 278 (2003) 1802-1806. [PMID: 12446723]
Accepted name: thebaine 6-O-demethylase
Reaction: thebaine + 2-oxoglutarate + O2 = neopinione + formaldehyde + succinate + CO2
Other name(s): T6ODM
Systematic name: thebaine,2-oxoglutarate:oxygen oxidoreductase (6-O-demethylating)
Comments: Requires Fe2+. Catalyses a step in morphine biosynthesis. The product neopinione spontaneously rearranges to the more stable codeinone. The enzyme also catalyses the 6-O-demethylation of oripavine to morphinone, with lower efficiency.
References:
1. Hagel, J.M. and Facchini, P.J. Dioxygenases catalyze the O-demethylation steps of morphine biosynthesis in opium poppy. Nat. Chem. Biol. 6 (2010) 273-275. [PMID: 20228795]
Accepted name: codeine 3-O-demethylase
Reaction: codeine + 2-oxoglutarate + O2 = morphine + formaldehyde + succinate + CO2
Other name(s): codeine O-demethylase; CODM
Systematic name: codeine,2-oxoglutarate:oxygen oxidoreductase (3-O-demethylating)
Comments: Requires Fe2+. Catalyses a step in morphine biosynthesis. The enzyme also catalyses the 3-O-demethylation of thebaine to oripavine, with lower efficiency.
References:
1. Hagel, J.M. and Facchini, P.J. Dioxygenases catalyze the O-demethylation steps of morphine biosynthesis in opium poppy. Nat. Chem. Biol. 6 (2010) 273-275. [PMID: 20228795]
Accepted name: 6-hydroxynicotinate 3-monooxygenase
Reaction: 6-hydroxynicotinate + NADH + H+ + O2 = 2,5-dihydroxypyridine + NAD+ + H2O + CO2
Other name(s): NicC; 6HNA monooxygenase; HNA-3-monooxygenase
Systematic name: 6-hydroxynicotinate,NADH:oxygen oxidoreductase (3-hydroxylating, decarboxylating)
Comments: A flavoprotein (FAD) [1]. The reaction is involved in the aerobic catabolism of nicotinic acid.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number:
References:
1. Nakano, H., Wieser, M., Hurh, B., Kawai, T., Yoshida, T., Yamane, T. and Nagasawa, T. Purification, characterization and gene cloning of 6-hydroxynicotinate 3-monooxygenase from Pseudomonas fluorescens TN5. Eur. J. Biochem. 260 (1999) 120-126. [PMID: 10091591]
2. Jimenez, J.I., Canales, A., Jimenez-Barbero, J., Ginalski, K., Rychlewski, L., Garcia, J.L. and Diaz, E. Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440. Proc. Natl. Acad. Sci. USA 105 (2008) 11329-11334. [PMID: 18678916]
Accepted name: angelicin synthase
Reaction: (+)-columbianetin + NADPH + H+ + O2 = angelicin + NADP+ + acetone + 2 H2O
Other name(s): CYP71AJ4 (gene name)
Systematic name: (+)-columbianetin,NADPH:oxygen oxidoreductase
Comments: This P450 monooxygenase enzyme is involved in the formation of angular furanocoumarins. Attacks its substrate by syn-elimination of hydrogen from C-3'.
References:
1. Larbat, R., Hehn, A., Hans, J., Schneider, S., Jugde, H., Schneider, B., Matern, U. and Bourgaud, F. Isolation and functional characterization of CYP71AJ4 encoding for the first P450 monooxygenase of angular furanocoumarin biosynthesis. J. Biol. Chem. 284 (2009) 4776-4785. [PMID: 19098286]
Accepted name: alkylglycerol monooxygenase
Reaction: 1-alkyl-sn-glycerol + tetrahydrobiopterin + O2 = 1-O-alkyl-sn-glycerol + dihydrobiopterin + H2O
Other name(s): glyceryl-ether monooxygenase; glyceryl-ether cleaving enzyme; alkylglycerol monooxygenase; glyceryl ether oxygenase; glyceryl etherase; O-alkylglycerol monooxygenase
Systematic name: 1-alkyl-sn-glycerol,tetrahydrobiopterin:oxygen oxidoreductase
Comments: The enzyme cleaves alkylglycerols, but does not cleave alkenylglycerols (plasmalogens). Requires reduced glutathione and phospholipids for full activity. The product spontaneously breaks down to form a fatty aldehyde and glycerol.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 37256-82-9
References:
1. Ishibashi, T. and Imai, Y. Solubilization and partial characterization of alkylglycerol monooxygenase from rat liver microsomes. Eur. J. Biochem. 132 (1983) 23-27. [PMID: 6840084]
2. Pfleger, E.C., Piantadosi, C. and Snyder, F. The biocleavage of isomeric glyceryl ethers by soluble liver enzymes in a variety of species. Biochim. Biophys. Acta 144 (1967) 633-648. [PMID: 4383918]
3. Snyder, F., Malone, B. and Piantadosi, C. Tetrahydropteridine-dependent cleavage enzyme for O-alkyl lipids: substrate specificity. Biochim. Biophys. Acta 316 (1973) 259-265. [PMID: 4355017]
4. Soodsma, J.F., Piantadosi, C. and Snyder, F. Partial characterization of the alkylglycerol cleavage enzyme system of rat liver. J. Biol. Chem. 247 (1972) 3923-3929. [PMID: 4402391]
5. Tietz, A., Lindberg, M. and Kennedy, E.P. A new pteridine-requiring enzyme system for the oxidation of glyceryl ethers. J. Biol. Chem. 239 (1964) 4081-4090. [PMID: 14247652]
6. Taguchi, H. and Armarego, W.L. Glyceryl-ether monooxygenase [EC 1.14.16.5]. A microsomal enzyme of ether lipid metabolism. Med. Res. Rev. 18 (1998) 43-89. [PMID: 9436181]
Accepted name: nicotinate dehydrogenase (cytochrome)
Reaction: nicotinate + a ferricytochrome + H2O = 6-hydroxynicotinate + a ferrocytochrome
Other name(s): nicotinic acid hydroxylase; nicotinate hydroxylase
Systematic name: nicotinate:cytochrome 6-oxidoreductase (hydroxylating)
Comments: This two-component enzyme from Pseudomonas belongs to the family of xanthine dehydrogenases, but differs from most other members of this family. While most members contain an FAD cofactor, the large subunit of this enzyme contains three c-type cytochromes, enabling it to interact with the electron transfer chain, probably by delivering the electrons to a cytochrome oxidase. The small subunit contains a typical molybdopterin cytosine dinucleotide(MCD) cofactor and two [2Fe-2S] clusters [1].
References:
1. Jimenez, J.I., Canales, A., Jimenez-Barbero, J., Ginalski, K., Rychlewski, L., Garcia, J.L. and Diaz, E. Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440. Proc. Natl. Acad. Sci. USA 105 (2008) 11329-11334. [PMID: 18678916]
2. Yang, Y., Yuan, S., Chen, T., Ma, P., Shang, G. and Dai, Y. Cloning, heterologous expression, and functional characterization of the nicotinate dehydrogenase gene from Pseudomonas putida KT2440. Biodegradation 20 (2009) 541-549. [PMID: 19118407]
Accepted name: 23S rRNA (uridine2552-2'-O-)-methyltransferase
Reaction: S-adenosyl-L-methionine + uridine2552 in 23S rRNA = S-adenosyl-L-homocysteine + 2'-O-methyluridine2552 in 23S rRNA
Other name(s): Um(2552) 23S ribosomal RNA methyltransferase; heat shock protein RrmJ; RrmJ; FTSJ; Um2552 methyltransferase
Systematic name: S-adenosyl-L-methionine:23S rRNA (uridine2552-2'-O-)-methyltransferase
Comments: The enzyme catalyses the 2'-O methylation of the universally conserved U2552 in the A loop of 23S rRNA [3].
References:
1. Caldas, T., Binet, E., Bouloc, P., Costa, A., Desgres, J. and Richarme, G. The FtsJ/RrmJ heat shock protein of Escherichia coli is a 23 S ribosomal RNA methyltransferase. J. Biol. Chem. 275 (2000) 16414-16419. [PMID: 10748051]
2. Hager, J., Staker, B.L., Bugl, H. and Jakob, U. Active site in RrmJ, a heat shock-induced methyltransferase. J. Biol. Chem. 277 (2002) 41978-41986. [PMID: 12181314]
3. Hager, J., Staker, B.L. and Jakob, U. Substrate binding analysis of the 23S rRNA methyltransferase RrmJ. J. Bacteriol. 186 (2004) 6634-6642. [PMID: 15375145]
4. Bugl, H., Fauman, E.B., Staker, B.L., Zheng, F., Kushner, S.R., Saper, M.A., Bardwell, J.C. and Jakob, U. RNA methylation under heat shock control. Mol. Cell 6 (2000) 349-360. [PMID: 10983982]
Accepted name: UDP-4-amino-4-deoxy-L-arabinose formyltransferase
Reaction: 10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-β-L-arabinopyranose = 5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-β-L-arabinopyranose
Other name(s): UDP-L-Ara4N formyltransferase; ArnAFT
Systematic name: 10-formyltetrahydrofolate:UDP-4-amino-4-deoxy-β-L-arabinose N-formyltransferase
Comments: The activity is part of a bifunctional enzyme also performing the reaction of EC 1.1.1.305 [UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating)].
References:
1. Breazeale, S.D., Ribeiro, A.A., McClerren, A.L. and Raetz, C.R.H. A formyltransferase required for polymyxin resistance in Escherichia coli and the modification of lipid A with 4-amino-4-deoxy-L-arabinose. Identification and function of UDP-4-deoxy-4-formamido-L-arabinose. J. Biol. Chem. 280 (2005) 14154-14167. [PMID: 15695810]
2. Gatzeva-Topalova, P.Z., May, A.P. and Sousa, M.C. Crystal structure and mechanism of the Escherichia coli ArnA (PmrI) transformylase domain. An enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance. Biochemistry 44 (2005) 5328-5338. [PMID: 15807526]
3. Williams, G.J., Breazeale, S.D., Raetz, C.R.H. and Naismith, J.H. Structure and function of both domains of ArnA, a dual function decarboxylase and a formyltransferase, involved in 4-amino-4-deoxy-L-arabinose biosynthesis. J. Biol. Chem. 280 (2005) 23000-23008. [PMID: 15809294]
4. Gatzeva-Topalova, P.Z., May, A.P. and Sousa, M.C. Structure and mechanism of ArnA: conformational change implies ordered dehydrogenase mechanism in key enzyme for polymyxin resistance. Structure 13 (2005) 929-942. [PMID: 15939024]
5. Yan, A., Guan, Z. and Raetz, C.R.H. An undecaprenyl phosphate-aminoarabinose flippase required for polymyxin resistance in Escherichia coli. J. Biol. Chem. 282 (2007) 36077-36089. [PMID: 17928292]
Accepted name: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
Reaction: (3R)-3-hydroxymyristoyl-[acyl-carrier protein] + UDP-3-O-[(3R)-3-hydroxymyristoyl]-α-D-glucosamine = UDP-2,3-bis[O-(3R)-3-hydroxymyristoyl]-α-D-glucosamine + a holo-[acyl-carrier protein]
Other name(s): UDP-3-O-acyl-glucosamine N-acyltransferase; UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase; acyltransferase LpxD; acyl-ACP:UDP-3-O-(3-hydroxyacyl)-GlcN N-acyltransferase; firA (gene name); lpxD (gene name)
Systematic name: (3R)-3-hydroxymyristoyl-[acyl-carrier protein]:UDP-3-O-[(3R)-3-hydroxymyristoyl]-α-D-glucosamine N-acetyltransferase
Comments: The enzyme catalyses a step of lipid A biosynthesis. LpxD from Escherichia prefers (R,S)-3-hydroxymyristoyl-[acyl-carrier protein] over (R,S)-3-hydroxypalmitoyl-[acyl-carrier protein] [1]. Escherichia coli lipid A acyltransferases do not have an absolute specificity for 14-carbon hydroxy fatty acids but can transfer fatty acids differing by one carbon unit if the fatty acid substrates are available. When grown on 1% propionic acid, lipid A also contains the odd-chain fatty acids tridecanoic acid, pentadecanoic acid, hydroxytridecanoic acid, and hydroxypentadecanoic acid [5].
References:
1. Bartling, C.M. and Raetz, C.R. Crystal structure and acyl chain selectivity of Escherichia coli LpxD, the N-acyltransferase of lipid A biosynthesis. Biochemistry 48 (2009) 8672-8683. [PMID: 19655786]
2. Buetow, L., Smith, T.K., Dawson, A., Fyffe, S. and Hunter, W.N. Structure and reactivity of LpxD, the N-acyltransferase of lipid A biosynthesis. Proc. Natl. Acad. Sci. USA 104 (2007) 4321-4326. [PMID: 17360522]
3. Bartling, C.M. and Raetz, C.R. Steady-state kinetics and mechanism of LpxD, the N-acyltransferase of lipid A biosynthesis. Biochemistry 47 (2008) 5290-5302. [PMID: 18422345]
4. Kelly, T.M., Stachula, S.A., Raetz, C.R. and Anderson, M.S. The firA gene of Escherichia coli encodes UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase. The third step of endotoxin biosynthesis. J. Biol. Chem. 268 (1993) 19866-19874. [PMID: 8366125]
5. Bainbridge, B.W., Karimi-Naser, L., Reife, R., Blethen, F., Ernst, R.K. and Darveau, R.P. Acyl chain specificity of the acyltransferases LpxA and LpxD and substrate availability contribute to lipid A fatty acid heterogeneity in Porphyromonas gingivalis. J. Bacteriol. 190 (2008) 4549-4558. [PMID: 18456814]
Accepted name: lipid II:glycine glycyltransferase
Reaction: N-acetylmuramoyl-L-alanyl-D-isoglutaminyl-L-lysyl-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine + glycyl-tRNA = N-acetylmuramoyl-L-alanyl-D-isoglutaminyl-L-lysyl-(N6-glycyl)-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine + tRNA
Other name(s): N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine:N6-glycine transferase; femX (gene name)
Systematic name: alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine:glycine N6-glycyltransferase
Comments: This enzyme from Staphylococcus aureus catalyses the transfer of glycine from a charged tRNA to N-acetylmuramoyl-L-alanyl-D-isoglutaminyl-L-lysyl-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine (lipid II), attaching it to the N6 of the L-lysine at position 3 of the pentapeptide. This is the first step in the synthesis of the pentaglycine interpeptide bridge that is used in S. aureus for the crosslinking of different glycan strands to each other. Four additional glycine residues are subsequently attached by EC 2.3.2.17 (FemA) and EC 2.3.2.18 (FemB).
References:
1. Schneider, T., Senn, M.M., Berger-Bachi, B., Tossi, A., Sahl, H.G. and Wiedemann, I. In vitro assembly of a complete, pentaglycine interpeptide bridge containing cell wall precursor (lipid II-Gly5) of Staphylococcus aureus. Mol. Microbiol. 53 (2004) 675-685. [PMID: 15228543]
Accepted name: N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-(N6-glycyl)-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine:glycine glycyltransferase
Reaction: N-acetylmuramoyl-L-alanyl-D-isoglutaminyl-L-lysyl-(N6-glycyl)-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine + 2 glycyl-tRNA = N-acetylmuramoyl-L-alanyl-D-isoglutaminyl-L-lysyl-(N6-triglycyl)-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine + 2 tRNA
Other name(s): femA (gene name)
Systematic name: N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-(N6-glycyl)-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine:glycine glycyltransferase
Comments: This enzyme catalyses the successive transfer of two glycine moieties from charged tRNAs to N-acetylmuramoyl-L-alanyl-D-isoglutaminyl-L-lysyl-(N6-glycyl)-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine, attaching them to a glycine residue previously attached by EC 2.3.2.16 (FemX) to the N6 of the L-lysine at position 3 of the pentapeptide. This is the second step in the synthesis of the pentaglycine interpeptide bridge that is used by Staphylococcus aureus for the crosslinking of different glycan strands to each other. The next step is catalysed by EC 2.3.2.18 (FemB). This enzyme is essential for methicillin resistance [1].
References:
1. Berger-Bachi, B., Barberis-Maino, L., Strassle, A. and Kayser, F.H. FemA, a host-mediated factor essential for methicillin resistance in Staphylococcus aureus: molecular cloning and characterization. Mol. Gen. Genet. 219 (1989) 263-269. [PMID: 2559314]
2. Johnson, S., Kruger, D. and Labischinski, H. FemA of Staphylococcus aureus: isolation and immunodetection. FEMS Microbiol. Lett. 132 (1995) 221-228. [PMID: 7590176]
3. Benson, T.E., Prince, D.B., Mutchler, V.T., Curry, K.A., Ho, A.M., Sarver, R.W., Hagadorn, J.C., Choi, G.H. and Garlick, R.L. X-ray crystal structure of Staphylococcus aureus FemA. Structure 10 (2002) 1107-1115. [PMID: 12176388]
4. Schneider, T., Senn, M.M., Berger-Bachi, B., Tossi, A., Sahl, H.G. and Wiedemann, I. In vitro assembly of a complete, pentaglycine interpeptide bridge containing cell wall precursor (lipid II-Gly5) of Staphylococcus aureus. Mol. Microbiol. 53 (2004) 675-685. [PMID: 15228543]
Accepted name: N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-(N6-triglycine)-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine:glycine glycyltransferase
Reaction: N-acetylmuramoyl-L-alanyl-D-isoglutaminyl-L-lysyl-(N6-triglycyl)-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine + 2 glycyl-tRNA = N-acetylmuramoyl-L-alanyl-D-isoglutaminyl-L-lysyl-(N6-pentaglycyl)-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine + 2 tRNA
Other name(s): femB (gene name)
Systematic name: N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-(N6-triglycine)-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine:glycine glycyltransferase
Comments: This Staphylococcus aureus enzyme catalyses the successive transfer of two glycine moieties from charged tRNAs to N-acetylmuramoyl-L-alanyl-D-isoglutaminyl-L-lysyl-(N6-triglycyl)-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine, attaching them to the three glycine molecules that were previously attached to the N6 of the L-lysine at position 3 of the pentapeptide by EC 2.3.2.16 (FemX) and EC 2.3.2.17 (FemA). This is the last step in the synthesis of the pentaglycine interpeptide bridge that is used in this organism for the crosslinking of different glycan strands to each other.
References:
1. Ehlert, K., Schroder, W. and Labischinski, H. Specificities of FemA and FemB for different glycine residues: FemB cannot substitute for FemA in staphylococcal peptidoglycan pentaglycine side chain formation. J. Bacteriol. 179 (1997) 7573-7576. [PMID: 9393725]
2. Rohrer, S. and Berger-Bachi, B. Application of a bacterial two-hybrid system for the analysis of protein-protein interactions between FemABX family proteins. Microbiology 149 (2003) 2733-2738. [PMID: 14523106]
3. Schneider, T., Senn, M.M., Berger-Bachi, B., Tossi, A., Sahl, H.G. and Wiedemann, I. In vitro assembly of a complete, pentaglycine interpeptide bridge containing cell wall precursor (lipid II-Gly5) of Staphylococcus aureus. Mol. Microbiol. 53 (2004) 675-685. [PMID: 15228543]
Accepted name: lipid IVA 3-deoxy-D-manno-octulosonic acid transferase
Reaction: 2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose + CMP-3-deoxy-D-manno-octulosonate = 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose + CMP
Glossary: lipid IVA = 2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose (KDO)-lipid IVA = 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
Other name(s): KDO transferase; waaA (gene name); kdtA (gene name); 3-deoxy-D-manno-oct-2-ulosonic acid transferase; 3-deoxy-manno-octulosonic acid transferase; lipid IVA KDO transferase
Systematic name: CMP-3-deoxy-D-manno-octulosonate:lipid IVA 3-deoxy-D-manno-octulosonate transferase
Comments: The bifunctional enzyme from Escherichia coli transfers two 3-deoxy-D-manno-octulosonate residues to lipid IVA (cf. EC 2.4.99.13 [(KDO)-lipid IVA 3-deoxy-D-manno-octulosonic acid transferase]) [1]. The monofunctional enzymes from Aquifex aeolicus and Haemophilus influenzae catalyse the transfer of a single 3-deoxy-D-manno-octulosonate residue from CMP-3-deoxy-D-manno-octulosonate to lipid IVA [2,3]. The enzymes from Chlamydia transfer three or more 3-deoxy-D-manno-octulosonate residues and generate genus-specific epitopes [4].
References:
1. Belunis, C.J. and Raetz, C.R. Biosynthesis of endotoxins. Purification and catalytic properties of 3-deoxy-D-manno-octulosonic acid transferase from Escherichia coli. J. Biol. Chem. 267 (1992) 9988-9997. [PMID: 1577828]
2. Mamat, U., Schmidt, H., Munoz, E., Lindner, B., Fukase, K., Hanuszkiewicz, A., Wu, J., Meredith, T.C., Woodard, R.W., Hilgenfeld, R., Mesters, J.R. and Holst, O. WaaA of the hyperthermophilic bacterium Aquifex aeolicus is a monofunctional 3-deoxy-D-manno-oct-2-ulosonic acid transferase involved in lipopolysaccharide biosynthesis. J. Biol. Chem. 284 (2009) 22248-22262. [PMID: 19546212]
3. White, K.A., Kaltashov, I.A., Cotter, R.J. and Raetz, C.R. A mono-functional 3-deoxy-D-manno-octulosonic acid (Kdo) transferase and a Kdo kinase in extracts of Haemophilus influenzae. J. Biol. Chem. 272 (1997) 16555-16563. [PMID: 9195966]
4. Lobau, S., Mamat, U., Brabetz, W. and Brade, H. Molecular cloning, sequence analysis, and functional characterization of the lipopolysaccharide biosynthetic gene kdtA encoding 3-deoxy-α-D-manno-octulosonic acid transferase of Chlamydia pneumoniae strain TW-183. Mol. Microbiol. 18 (1995) 391-399. [PMID: 8748024]
Accepted name: (KDO)-lipid IVA 3-deoxy-D-manno-octulosonic acid transferase
Reaction: 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose + CMP-3-deoxy-D-manno-octulosonate = 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose + CMP
Glossary: (KDO)-lipid IVA = 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose (KDO)2-lipid IVA = 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
Other name(s): KDO transferase; waaA (gene name); kdtA (gene name); Kdo transferase; 3-deoxy-D-manno-oct-2-ulosonic acid transferase; 3-deoxy-manno-octulosonic acid transferase
Systematic name: CMP-3-deoxy-D-manno-octulosonate:(KDO)-lipid IVA 3-deoxy-D-manno-octulosonate transferase
Comments: The bifunctional enzyme from Escherichia coli transfers two 3-deoxy-D-manno-octulosonate residues to lipid IVA (cf. EC 2.4.99.12 [lipid IVA 3-deoxy-D-manno-octulosonic acid transferase]) [1]. The enzymes from Chlamydia transfer three or more 3-deoxy-D-manno-octulosonate residues and generate genus-specific epitopes [4].
References:
1. Belunis, C.J. and Raetz, C.R. Biosynthesis of endotoxins. Purification and catalytic properties of 3-deoxy-D-manno-octulosonic acid transferase from Escherichia coli. J. Biol. Chem. 267 (1992) 9988-9997. [PMID: 1577828]
2. Lobau, S., Mamat, U., Brabetz, W. and Brade, H. Molecular cloning, sequence analysis, and functional characterization of the lipopolysaccharide biosynthetic gene kdtA encoding 3-deoxy-α-D-manno-octulosonic acid transferase of Chlamydia pneumoniae strain TW-183. Mol. Microbiol. 18 (1995) 391-399. [PMID: 8748024]
Accepted name: (KDO)2-lipid IVA (2-8) 3-deoxy-D-manno-octulosonic acid transferase
Reaction: 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose + CMP-3-deoxy-D-manno-octulosonate = 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→8)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)-3-deoxy-α-D-manno-oct-2-ulopyranosy[l-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyrano]syl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanoyl]amino-1-O-phosphono-α-D-glucopyranose + CMP
Glossary: (KDO)2-lipid IVA = 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose (KDO)3-lipid IVA = 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→8)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
Other name(s): KDO transferase; waaA (gene name); kdtA (gene name); 3-deoxy-D-manno-oct-2-ulosonic acid transferase; 3-deoxy-manno-octulosonic acid transferase
Systematic name: CMP-3-deoxy-D-manno-octulosonate:(KDO)2-lipid IVA 3-deoxy-D-manno-octulosonate transferase ((2→8) glycosidic bond-forming)
Comments: The enzymes from Chlamydia transfer three or more 3-deoxy-D-manno-octulosonate residues and generate genus-specific epitopes.
References:
1. Lobau, S., Mamat, U., Brabetz, W. and Brade, H. Molecular cloning, sequence analysis, and functional characterization of the lipopolysaccharide biosynthetic gene kdtA encoding 3-deoxy-α-D-manno-octulosonic acid transferase of Chlamydia pneumoniae strain TW-183. Mol. Microbiol. 18 (1995) 391-399. [PMID: 8748024]
2. Mamat, U., Baumann, M., Schmidt, G. and Brade, H. The genus-specific lipopolysaccharide epitope of Chlamydia is assembled in C. psittaci and C. trachomatis by glycosyltransferases of low homology. Mol. Microbiol. 10 (1993) 935-941. [PMID: 7523826]
3. Belunis, C.J., Mdluli, K.E., Raetz, C.R. and Nano, F.E. A novel 3-deoxy-D-manno-octulosonic acid transferase from Chlamydia trachomatis required for expression of the genus-specific epitope. J. Biol. Chem. 267 (1992) 18702-18707. [PMID: 1382060]
Accepted name: (KDO)3-lipid IVA (2-4) 3-deoxy-D-manno-octulosonic acid transferase
Reaction: 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→8)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose + CMP-3-deoxy-D-manno-octulosonate = 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→8)-[3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)]-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose + CMP
Glossary: (KDO)3-lipid IVA = 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→8)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose (KDO)4-lipid IVA = 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→8)-[3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
Other name(s): KDO transferase; waaA (gene name); kdtA (gene name); 3-deoxy-D-manno-oct-2-ulosonic acid transferase; 3-deoxy-manno-octulosonic acid transferase
Systematic name: CMP-3-deoxy-D-manno-octulosonate:(KDO)3-lipid IVA 3-deoxy-D-manno-octulosonate transferase ((2→4) glycosidic bond-forming)
Comments: The enzyme from Chlamydia psittaci transfers four KDO residues to lipid A, forming a branched tetrasaccharide with the structure α-KDO-(2,8)-[α-KDO-(2,4)]-α-KDO-(2,4)-α-KDO (cf. EC 2.4.99.12 [lipid IVA 3-deoxy-D-manno-octulosonic acid transferase], EC 2.4.99.13 [(KDO)-lipid IVA 3-deoxy-D-manno-octulosonic acid transferase], and EC 2.4.99.14 [(KDO)2-lipid IVA (2-8) 3-deoxy-D-manno-octulosonic acid transferase]).
References:
1. Brabetz, W., Lindner, B. and Brade, H. Comparative analyses of secondary gene products of 3-deoxy-D-manno-oct-2-ulosonic acid transferases from Chlamydiaceae in Escherichia coli K-12 . Eur. J. Biochem. 267 (2000) 5458-5465. [PMID: 10951204]
2. Holst, O., Bock, K., Brade, L. and Brade, H. The structures of oligosaccharide bisphosphates isolated from the lipopolysaccharide of a recombinant Escherichia coli strain expressing the gene gseA [3-deoxy-D-manno-octulopyranosonic acid (Kdo) transferase] of Chlamydia psittaci 6BC . Eur. J. Biochem. 229 (1995) 194-200. [PMID: 7744029]
Accepted name: 4-hydroxybenzoate polyprenyltransferase
Reaction: a polyprenyl diphosphate + 4-hydroxybenzoate = diphosphate + a 4-hydroxy-3-polyprenylbenzoate
Other name(s): nonaprenyl-4-hydroxybenzoate transferase; 4-hydroxybenzoate transferase; p-hydroxybenzoate dimethylallyltransferase; p-hydroxybenzoate polyprenyltransferase; p-hydroxybenzoic acid-polyprenyl transferase; p-hydroxybenzoic-polyprenyl transferase; 4-hydroxybenzoate nonaprenyltransferase
Systematic name: polyprenyl-diphosphate:4-hydroxybenzoate polyprenyltransferase
Comments: This enzyme, involved in the biosynthesis of ubiquinone, attaches a polyprenyl side chain to a 4-hydroxybenzoate ring, producing the first ubiquinone intermediate that is membrane bound. The number of isoprenoid subunits in the side chain varies in different species. The enzyme does not have any specificity concerning the length of the polyprenyl tail, and accepts tails of various lengths with similar efficiency [2,4,5].
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 9030-77-7
References:
1. Kalén, A., Appelkvist, E.-L., Chojnacki, T. and Dallner, G. Nonaprenyl-4-hydroxybenzoate transferase, an enzyme involved in ubiquinone biosynthesis, in the endoplasmic reticulum-Golgi system of rat liver. J. Biol. Chem. 265 (1990) 1158-1164. [PMID: 2295606]
2. Melzer, M. and Heide, L. Characterization of polyprenyldiphosphate: 4-hydroxybenzoate polyprenyltransferase from Escherichia coli. Biochim. Biophys. Acta 1212 (1994) 93-102. [PMID: 8155731]
3. Okada, K., Ohara, K., Yazaki, K., Nozaki, K., Uchida, N., Kawamukai, M., Nojiri, H. and Yamane, H. The AtPPT1 gene encoding 4-hydroxybenzoate polyprenyl diphosphate transferase in ubiquinone biosynthesis is required for embryo development in Arabidopsis thaliana. Plant Mol. Biol. 55 (2004) 567-577. [PMID: 15604701]
4. Forsgren, M., Attersand, A., Lake, S., Grunler, J., Swiezewska, E., Dallner, G. and Climent, I. Isolation and functional expression of human COQ2, a gene encoding a polyprenyl transferase involved in the synthesis of CoQ. Biochem. J. 382 (2004) 519-526. [PMID: 15153069]
5. Tran, U.C. and Clarke, C.F. Endogenous synthesis of coenzyme Q in eukaryotes. Mitochondrion 7 Suppl (2007) S62-S71. [PMID: 17482885]
Accepted name: UDP-4-amino-4-deoxy-L-arabinose aminotransferase
Reaction: UDP-4-amino-4-deoxy-β-L-arabinopyranose + 2-oxoglutarate = UDP-β-L-threo-pentapyranos-4-ulose + L-glutamate
Other name(s): UDP-(β-L-threo-pentapyranosyl-4"-ulose diphosphate) aminotransferase; UDP-4-amino-4-deoxy-L-arabinose—oxoglutarate aminotransferase; UDP-Ara4O aminotransferase; UDP-L-Ara4N transaminase
Systematic name: UDP-4-amino-4-deoxy-β-L-arabinose:2-oxoglutarate aminotransferase
Comments: A pyridoxal 5'-phosphate enzyme.
References:
1. Breazeale, S.D., Ribeiro, A.A. and Raetz, C.R. Origin of lipid A species modified with 4-amino-4-deoxy-L-arabinose in polymyxin-resistant mutants of Escherichia coli. An aminotransferase (ArnB) that generates UDP-4-deoxyl-L-arabinose. J. Biol. Chem. 278 (2003) 24731-24739. [PMID: 12704196]
2. Noland, B.W., Newman, J.M., Hendle, J., Badger, J., Christopher, J.A., Tresser, J., Buchanan, M.D., Wright, T.A., Rutter, M.E., Sanderson, W.E., Muller-Dieckmann, H.J., Gajiwala, K.S. and Buchanan, S.G. Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: a 4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying enzyme. Structure 10 (2002) 1569-1580. [PMID: 12429098]
Accepted name: 3-deoxy-D-manno-octulosonic acid kinase
Reaction: 3-deoxy-α-D-manno-oct-2-ulopyranonosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose + ATP = 3-deoxy-4-O-phosphono-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose + ADP
Glossary: (KDO)-lipid IVA = 3-deoxy-α-D-manno-oct-2-ulopyranonosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose (4-O-phospho-KDO)-lipid IVA = 3-deoxy-4-O-phosphono-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
Other name(s): kdkA (gene name); Kdo kinase
Systematic name: ATP:(KDO)-lipid IVA 3-deoxy-α-D-manno-oct-2-ulopyranose 4-phosphotransferase
Comments: The enzyme phosphorylates the 4-OH position of KDO in (KDO)-lipid IVA.
References:
1. Brabetz, W., Muller-Loennies, S. and Brade, H. 3-Deoxy-D-manno-oct-2-ulosonic acid (Kdo) transferase (WaaA) and kdo kinase (KdkA) of Haemophilus influenzae are both required to complement a waaA knockout mutation of Escherichia coli. J. Biol. Chem. 275 (2000) 34954-34962. [PMID: 10952982]
2. Harper, M., Boyce, J.D., Cox, A.D., St Michael, F., Wilkie, I.W., Blackall, P.J. and Adler, B. Pasteurella multocida expresses two lipopolysaccharide glycoforms simultaneously, but only a single form is required for virulence: identification of two acceptor-specific heptosyl I transferases. Infect. Immun. 75 (2007) 3885-3893. [PMID: 17517879]
3. White, K.A., Kaltashov, I.A., Cotter, R.J. and Raetz, C.R. A mono-functional 3-deoxy-D-manno-octulosonic acid (Kdo) transferase and a Kdo kinase in extracts of Haemophilus influenzae. J. Biol. Chem. 272 (1997) 16555-16563. [PMID: 9195966]
4. White, K.A., Lin, S., Cotter, R.J. and Raetz, C.R. A Haemophilus influenzae gene that encodes a membrane bound 3-deoxy-D-manno-octulosonic acid (Kdo) kinase. Possible involvement of kdo phosphorylation in bacterial virulence. J. Biol. Chem. 274 (1999) 31391-31400. [PMID: 10531340]
Accepted name: D-glycero-β-D-manno-heptose-7-phosphate kinase
Reaction: D-glycero-D-manno-heptose 7-phosphate + ATP = D-glycero-β-D-manno-heptose 1,7-bisphosphate + ADP
Other name(s): heptose 7-phosphate kinase; D-β-D-heptose 7-phosphotransferase; D-β-D-heptose-7-phosphate kinase; HldE1 heptokinase; glycero-manno-heptose 7-phosphate kinase; D-β-D-heptose 7-phosphate kinase/D-β-D-heptose 1-phosphate adenylyltransferase; hldE (gene name); rfaE (gene name)
Systematic name: ATP:D-glycero-β-D-manno-heptose 7-phosphate 1-phosphotransferase
Comments: The bifunctional protein hldE includes D-glycero-β-D-manno-heptose-7-phosphate kinase and D-glycero-β-D-manno-heptose 1-phosphate adenylyltransferase activity (cf. EC 2.7.7.70). The enzyme is involved in biosynthesis of ADP-L-glycero-β-D-manno-heptose, which is utilized for assembly of the lipopolysaccharide inner core in Gram-negative bacteria. The enzyme selectively produces D-glycero-β-D-manno-heptose 1,7-bisphosphate [5].
References:
1. McArthur, F., Andersson, C.E., Loutet, S., Mowbray, S.L. and Valvano, M.A. Functional analysis of the glycero-manno-heptose 7-phosphate kinase domain from the bifunctional HldE protein, which is involved in ADP-L-glycero-D-manno-heptose biosynthesis. J. Bacteriol. 187 (2005) 5292-5300. [PMID: 16030223]
2. Kneidinger, B., Marolda, C., Graninger, M., Zamyatina, A., McArthur, F., Kosma, P., Valvano, M.A. and Messner, P. Biosynthesis pathway of ADP-L-glycero-β-D-manno-heptose in Escherichia coli. J. Bacteriol. 184 (2002) 363-369. [PMID: 11751812]
3. Valvano, M.A., Messner, P. and Kosma, P. Novel pathways for biosynthesis of nucleotide-activated glycero-manno-heptose precursors of bacterial glycoproteins and cell surface polysaccharides. Microbiology 148 (2002) 1979-1989. [PMID: 12101286]
4. Jin, U.H., Chung, T.W., Lee, Y.C., Ha, S.D. and Kim, C.H. Molecular cloning and functional expression of the rfaE gene required for lipopolysaccharide biosynthesis in Salmonella typhimurium. Glycoconj. J. 18 (2001) 779-787. [PMID: 12441667]
5. Wang, L., Huang, H., Nguyen, H.H., Allen, K.N., Mariano, P.S. and Dunaway-Mariano, D. Divergence of biochemical function in the HAD superfamily: D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB). Biochemistry 49 (2010) 1072-1081. [PMID: 20050615]
Accepted name: D-glycero-α-D-manno-heptose-7-phosphate kinase
Reaction: D-glycero-α-D-manno-heptose 7-phosphate + ATP = D-glycero-α-D-manno-heptose 1,7-bisphosphate + ADP
Other name(s): D-α-D-heptose-7-phosphate kinase; hdda (gene name); gmhB (gene name)
Systematic name: ATP:D-glycero-α-D-manno-heptose 7-phosphate 1-phosphotransferase
Comments: The enzyme is involved in biosynthesis of GDP-D-glycero-α-D-manno-heptose, which is required for assembly of S-layer glycoprotein in Gram-positive bacteria. The enzyme is specific for the α-anomer.
References:
1. Kneidinger, B., Graninger, M., Puchberger, M., Kosma, P. and Messner, P. Biosynthesis of nucleotide-activated D-glycero-D-manno-heptose. J. Biol. Chem. 276 (2001) 20935-20944. [PMID: 11279237]
2. Valvano, M.A., Messner, P. and Kosma, P. Novel pathways for biosynthesis of nucleotide-activated glycero-manno-heptose precursors of bacterial glycoproteins and cell surface polysaccharides. Microbiology 148 (2002) 1979-1989. [PMID: 12101286]
Accepted name: D-glycero-β-D-manno-heptose 1-phosphate adenylyltransferase
Reaction: D-glycero-β-D-manno-heptose 1-phosphate + ATP = ADP-D-glycero-β-D-manno-heptose + diphosphate
Other name(s): D-β-D-heptose 7-phosphate kinase/D-β-D-heptose 1-phosphate adenylyltransferase; D-glycero-D-manno-heptose-1β-phosphate adenylyltransferase; hldE (gene name); rfaE (gene name)
Systematic name: ATP:D-glycero-β-D-manno-heptose 1-phosphate adenylyltransferase
Comments: The bifunctional protein hldE includes D-glycero-β-D-manno-heptose-7-phosphate kinase and D-glycero-β-D-manno-heptose 1-phosphate adenylyltransferase activity (cf. EC 2.7.1.167). The enzyme is involved in biosynthesis of ADP-L-glycero-β-D-manno-heptose, which is utilized for assembly of the lipopolysaccharide inner core in Gram-negative bacteria.
References:
1. Valvano, M.A., Marolda, C.L., Bittner, M., Glaskin-Clay, M., Simon, T.L. and Klena, J.D. The rfaE gene from Escherichia coli encodes a bifunctional protein involved in biosynthesis of the lipopolysaccharide core precursor ADP-L-glycero-D-manno-heptose. J. Bacteriol. 182 (2000) 488-497. [PMID: 10629197]
2. Kneidinger, B., Marolda, C., Graninger, M., Zamyatina, A., McArthur, F., Kosma, P., Valvano, M.A. and Messner, P. Biosynthesis pathway of ADP-L-glycero-β-D-manno-heptose in Escherichia coli. J. Bacteriol. 184 (2002) 363-369. [PMID: 11751812]
3. Valvano, M.A., Messner, P. and Kosma, P. Novel pathways for biosynthesis of nucleotide-activated glycero-manno-heptose precursors of bacterial glycoproteins and cell surface polysaccharides. Microbiology 148 (2002) 1979-1989. [PMID: 12101286]
4. Wang, L., Huang, H., Nguyen, H.H., Allen, K.N., Mariano, P.S. and Dunaway-Mariano, D. Divergence of biochemical function in the HAD superfamily: D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB). Biochemistry 49 (2010) 1072-1081. [PMID: 20050615]
Accepted name: D-glycero-α-D-manno-heptose 1-phosphate guanylyltransferase
Reaction: D-glycero-α-D-manno-heptose 1-phosphate + GTP = GDP-D-glycero-α-D-manno-heptose + diphosphate
Other name(s): hddC (gene name); gmhD (gene name)
Systematic name: GTP:D-glycero-α-D-manno-heptose 1-phosphate guanylyltransferase
Comments: The enzyme is involved in biosynthesis of GDP-D-glycero-α-D-manno-heptose, which is required for assembly of S-layer glycoprotein in some Gram-positive bacteria.
References:
1. Kneidinger, B., Graninger, M., Puchberger, M., Kosma, P. and Messner, P. Biosynthesis of nucleotide-activated D-glycero-D-manno-heptose. J. Biol. Chem. 276 (2001) 20935-20944. [PMID: 11279237]
Accepted name: phosphatidate phosphatase
Reaction: a 1,2-diacylglycerol 3-phosphate + H2O = a 1,2-diacyl-sn-glycerol + phosphate
Glossary: a 1,2-diacylglycerol 3-phosphate = a 3-sn-phosphatidate a 1,2-diacyl-sn-glycerol = DAG
Other name(s): phosphatic acid phosphatase; acid phosphatidyl phosphatase; phosphatic acid phosphohydrolase; PAP, Lipin
Systematic name: diacylglycerol-3-phosphate phosphohydrolase
Comments: This enzyme catalyses the Mg2+-dependent dephosphorylation of a 1,2-diacylglycerol-3-phosphate, yielding a 1,2-diacyl-sn-glycerol (DAG), the substrate for de novo lipid synthesis via the Kennedy pathway and for the synthesis of triacylglycerol. In lipid signaling, the enzyme generates a pool of DAG to be used for protein kinase C activation. The mammalian enzymes are known as lipins.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 9025-77-8
References:
1. Smith, S.W., Weiss, S.B. and Kennedy, E.P. The enzymatic dephosphorylation of phosphatidic acids. J. Biol. Chem. 228 (1957) 915-922. [PMID: 13475370]
2. Carman, G.M. and Han, G.S. Phosphatidic acid phosphatase, a key enzyme in the regulation of lipid synthesis. J. Biol. Chem. 284 (2009) 2593-2597. [PMID: 18812320]
Accepted name: diacylglycerol diphosphate phosphatase
Reaction: 1,2-diacyl-sn-glycerol 3-diphosphate + H2O = 1,2-diacyl-sn-glycerol 3-phosphate + phosphate
Other name(s): DGPP phosphatase; DGPP phosphohydrolase; DPP1; DPPL1; DPPL2; PAP2; pyrophosphate phosphatase
Systematic name: 1,2-diacyl-sn-glycerol 3-phosphate phosphohydrolase
Comments: The bifunctional enzyme catalyses the dephosphorylation of diacylglycerol diphosphate to phosphatidate and the subsequent dephosphorylation of phosphatidate to diacylglycerol (cf. phosphatidate phosphatase (EC 3.1.3.4)). It regulates intracellular levels of diacylglycerol diphosphate and phosphatidate, phospholipid molecules believed to play a signaling role in stress response [6]. The phosphatase activity of the bifunctional enzyme is Mg2+-independent and N-ethylmaleimide-insensitive and is distinct from the Mg2+-dependent and N-ethylmaleimide-sensitive enzyme EC 3.1.3.4 (phosphatidate phosphatase) [5].The diacylglycerol pyrophosphate phosphatase activity in Saccharomyces cerevisiae is induced by zinc depletion, by inositol supplementation, and when cells enter the stationary phase [4].
References:
1. Dillon, D.A., Wu, W.I., Riedel, B., Wissing, J.B., Dowhan, W. and Carman, G.M. The Escherichia coli pgpB gene encodes for a diacylglycerol pyrophosphate phosphatase activity. J. Biol. Chem. 271 (1996) 30548-30553. [PMID: 8940025]
2. Dillon, D.A., Chen, X., Zeimetz, G.M., Wu, W.I., Waggoner, D.W., Dewald, J., Brindley, D.N. and Carman, G.M. Mammalian Mg2+-independent phosphatidate phosphatase (PAP2) displays diacylglycerol pyrophosphate phosphatase activity. J. Biol. Chem. 272 (1997) 10361-10366. [PMID: 9099673]
3. Wu, W.I., Liu, Y., Riedel, B., Wissing, J.B., Fischl, A.S. and Carman, G.M. Purification and characterization of diacylglycerol pyrophosphate phosphatase from Saccharomyces cerevisiae. J. Biol. Chem. 271 (1996) 1868-1876. [PMID: 8567632]
4. Oshiro, J., Han, G.S. and Carman, G.M. Diacylglycerol pyrophosphate phosphatase in Saccharomyces cerevisiae. Biochim. Biophys. Acta 1635 (2003) 1-9. [PMID: 14642771]
5. Carman, G.M. Phosphatidate phosphatases and diacylglycerol pyrophosphate phosphatases in Saccharomyces cerevisiae and Escherichia coli. Biochim. Biophys. Acta 1348 (1997) 45-55. [PMID: 9370315]
6. Han, G.S., Johnston, C.N., Chen, X., Athenstaedt, K., Daum, G. and Carman, G.M. Regulation of the Saccharomyces cerevisiae DPP1-encoded diacylglycerol pyrophosphate phosphatase by zinc. J. Biol. Chem. 276 (2001) 10126-10133. [PMID: 11139591]
Accepted name: D-glycero-β-D-manno-heptose 1,7-bisphosphate 7-phosphatase
Reaction: D-glycero-β-D-manno-heptose 1,7-bisphosphate + H2O = D-glycero-β-D-manno-heptose 1-phosphate + phosphate
Other name(s): gmhB (gene name); yaeD (gene name)
Systematic name: D-glycero-β-D-manno-heptose 1,7-bisphosphate 7-phosphohydrolase
Comments: The enzyme is involved in biosynthesis of ADP-L-glycero-β-D-manno-heptose, which is utilized for assembly of the lipopolysaccharide inner core in Gram-negative bacteria. In vitro the catalytic efficiency with the β-anomer is 100-200-fold higher than with the α-anomer [3].
References:
1. Kneidinger, B., Marolda, C., Graninger, M., Zamyatina, A., McArthur, F., Kosma, P., Valvano, M.A. and Messner, P. Biosynthesis pathway of ADP-L-glycero-β-D-manno-heptose in Escherichia coli. J. Bacteriol. 184 (2002) 363-369. [PMID: 11751812]
2. Valvano, M.A., Messner, P. and Kosma, P. Novel pathways for biosynthesis of nucleotide-activated glycero-manno-heptose precursors of bacterial glycoproteins and cell surface polysaccharides. Microbiology 148 (2002) 1979-1989. [PMID: 12101286]
3. Wang, L., Huang, H., Nguyen, H.H., Allen, K.N., Mariano, P.S. and Dunaway-Mariano, D. Divergence of biochemical function in the HAD superfamily: D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB) . Biochemistry 49 (2010) 1072-1081. [PMID: 20050615]
Accepted name: D-glycero-α-D-manno-heptose 1,7-bisphosphate 7-phosphatase
Reaction: D-glycero-α-D-manno-heptose 1,7-bisphosphate + H2O = D-glycero-α-D-manno-heptose 1-phosphate + phosphate
Other name(s): gmhB (gene name)
Systematic name: D-glycero-α-D-manno-heptose 1,7-bisphosphate 7-phosphohydrolase
Comments: The enzyme is involved in biosynthesis of GDP-D-glycero-α-D-manno-heptose, which is required for assembly of S-layer glycoprotein in some Gram-positive bacteria. The in vitro catalytic efficiency of the enzyme from Bacteroides thetaiotaomicron is 6-fold higher with the α-anomer than with the β-anomer [1].
References:
1. Wang, L., Huang, H., Nguyen, H.H., Allen, K.N., Mariano, P.S. and Dunaway-Mariano, D. Divergence of biochemical function in the HAD superfamily: D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB). Biochemistry 49 (2010) 1072-1081. [PMID: 20050615]
Accepted name: peptidoglycan-N-acetylglucosamine deacetylase
Reaction: peptidoglycan-N-acetyl-D-glucosamine + H2O = peptidoglycan-D-glucosamine + acetate
Other name(s): HP310; PgdA; SpPgdA; BC1960; peptidoglycan deacetylase; N-acetylglucosamine deacetylase; peptidoglycan GlcNAc deacetylase; peptidoglycan N-acetylglucosamine deacetylase; PG N-deacetylase
Systematic name: peptidoglycan-N-acetylglucosamine amidohydrolase
Comments: Modification of peptidoglycan by N-deacetylation is an important factor in virulence of Helicobacter pylori, Listeria monocytogenes and Streptococcus suis [4-6]. The enzyme from Streptococcus pneumoniae is a metalloenzyme using a His-His-Asp zinc-binding triad with a nearby aspartic acid and histidine acting as the catalytic base and acid, respectively [3].
References:
1. Psylinakis, E., Boneca, I.G., Mavromatis, K., Deli, A., Hayhurst, E., Foster, S.J., Varum, K.M. and Bouriotis, V. Peptidoglycan N-acetylglucosamine deacetylases from Bacillus cereus, highly conserved proteins in Bacillus anthracis. J. Biol. Chem. 280 (2005) 30856-30863. [PMID: 15961396]
2. Tsalafouta, A., Psylinakis, E., Kapetaniou, E.G., Kotsifaki, D., Deli, A., Roidis, A., Bouriotis, V. and Kokkinidis, M. Purification, crystallization and preliminary X-ray analysis of the peptidoglycan N-acetylglucosamine deacetylase BC1960 from Bacillus cereus in the presence of its substrate (GlcNAc)6. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 203-205. [PMID: 18323609]
3. Blair, D.E., Schuttelkopf, A.W., MacRae, J.I. and van Aalten, D.M. Structure and metal-dependent mechanism of peptidoglycan deacetylase, a streptococcal virulence factor. Proc. Natl. Acad. Sci. USA 102 (2005) 15429-15434. [PMID: 16221761]
4. Wang, G., Olczak, A., Forsberg, L.S. and Maier, R.J. Oxidative stress-induced peptidoglycan deacetylase in Helicobacter pylori. J. Biol. Chem. 284 (2009) 6790-6800. [PMID: 19147492]
5. Popowska, M., Kusio, M., Szymanska, P. and Markiewicz, Z. Inactivation of the wall-associated de-N-acetylase (PgdA) of Listeria monocytogenes results in greater susceptibility of the cells to induced autolysis. J Microbiol Biotechnol 19 (2009) 932-945. [PMID: 19809250]
6. Fittipaldi, N., Sekizaki, T., Takamatsu, D., de la Cruz Domínguez-Punaro, M., Harel, J., Bui, N.K., Vollmer, W. and Gottschalk, M. Significant contribution of the pgdA gene to the virulence of Streptococcus suis. Mol. Microbiol. 70 (2008) 1120-1135. [PMID: 18990186]
Accepted name: chitin disaccharide deacetylase
Reaction: 2-(acetylamino)-4-O-[2-(acetylamino)-2-deoxy-β-D-glucopyranosyl]-2-deoxy-β-D-glucopyranose + H2O = 2-(acetylamino)-4-O-(2-amino-2-deoxy-β-D-glucopyranosyl)-2-deoxy-β-D-glucopyranose + acetate
Other name(s): chitobiose amidohydolase; COD; chitin oligosaccharide deacetylase; chitin oligosaccharide amidohydolase
Systematic name: 2-(acetylamino)-4-O-[2-(acetylamino)-2-deoxy-β-D-glucopyranosyl]-2-deoxy-D-glucopyranose acetylhydrolase
Comments: Chitin oligosaccharide deacetylase is a key enzyme in the chitin catabolic cascade of chitinolytic Vibrio strains. Besides being a nutrient, the heterodisaccharide product 4-O-(N-acetyl-β-D-glucosaminyl)-D-glucosamine is a unique inducer of chitinase production in Vibrio parahaemolyticus [2]. In contrast to EC 3.5.1.41 (chitin deacetylase) this enzyme is specific for the chitin disaccharide [1,3]. It also deacetylates the chitin trisaccharide with lower efficiency [3]. No activity with higher polymers of GlcNAc [1,3].
References:
1. Kadokura, K., Rokutani, A., Yamamoto, M., Ikegami, T., Sugita, H., Itoi, S., Hakamata, W., Oku, T. and Nishio, T. Purification and characterization of Vibrio parahaemolyticus extracellular chitinase and chitin oligosaccharide deacetylase involved in the production of heterodisaccharide from chitin. Appl. Microbiol. Biotechnol. 75 (2007) 357-365. [PMID: 17334758]
2. Hirano, T., Kadokura, K., Ikegami, T., Shigeta, Y., Kumaki, Y., Hakamata, W., Oku, T. and Nishio, T. Heterodisaccharide 4-O-(N-acetyl-β-D-glucosaminyl)-D-glucosamine is a specific inducer of chitinolytic enzyme production in Vibrios harboring chitin oligosaccharide deacetylase genes. Glycobiology 19 (2009) 1046-1053. [PMID: 19553519]
3. Ohishi, K., Yamagishi, M., Ohta, T., Motosugi, M., Izumida, H., Sano, H., Adachi, K., Miwa, T. Purification and properties of two deacetylases produced by Vibrio alginolyticus H-8. Biosci. Biotechnol. Biochem. 61 (1997) 1113-1117.
4. Ohishi, K., Murase, K., Ohta, T. and Etoh, H. Cloning and sequencing of the deacetylase gene from Vibrio alginolyticus H-8. J. Biosci. Bioeng. 90 (2000) 561-563. [PMID: 16232910]
Accepted name: N-formylmaleamate deformylase
Reaction: N-formylmaleamic acid + H2O = maleamate + formate
Other name(s): NicD
Systematic name: N-formylmaleamic acid amidohydrolase
Comments: The reaction is involved in the aerobic catabolism of nicotinic acid.
References:
1. Jimenez, J.I., Canales, A., Jimenez-Barbero, J., Ginalski, K., Rychlewski, L., Garcia, J.L. and Diaz, E. Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440. Proc. Natl. Acad. Sci. USA 105 (2008) 11329-11334. [PMID: 18678916]
Accepted name: maleamate amidohydrolase
Reaction: maleamate + H2O = maleate + NH3
Other name(s): NicF
Systematic name: maleamate amidohydrolase
Comments: The reaction is involved in the aerobic catabolism of nicotinic acid.
References:
1. Jimenez, J.I., Canales, A., Jimenez-Barbero, J., Ginalski, K., Rychlewski, L., Garcia, J.L. and Diaz, E. Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440. Proc. Natl. Acad. Sci. USA 105 (2008) 11329-11334. [PMID: 18678916]
Accepted name: UDP-3-O-acyl-N-acetylglucosamine deacetylase
Reaction: UDP-3-O-[(3R)-3-hydroxymyristoyl]-N-acetylglucosamine + H2O = UDP-3-O-[(3R)-3-hydroxymyristoyl]-D-glucosamine + acetate
Other name(s): LpxC protein; LpxC enzyme; LpxC deacetylase; deacetylase LpxC; UDP-3-O-acyl-GlcNAc deacetylase; UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase; UDP-(3-O-acyl)-N-acetylglucosamine deacetylase; UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase; UDP-(3-O-(R-3-hydroxymyristoyl))-N-acetylglucosamine deacetylase
Systematic name: UDP-3-O-[(3R)-3-hydroxymyristoyl]-N-acetylglucosamine amidohydrolase
Comments: A zinc protein. The enzyme catalyses a committed step in the biosynthesis of lipid A.
References:
1. Hernick, M., Gennadios, H.A., Whittington, D.A., Rusche, K.M., Christianson, D.W. and Fierke, C.A. UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase functions through a general acid-base catalyst pair mechanism. J. Biol. Chem. 280 (2005) 16969-16978. [PMID: 15705580]
2. Jackman, J.E., Raetz, C.R. and Fierke, C.A. UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase of Escherichia coli is a zinc metalloenzyme. Biochemistry 38 (1999) 1902-1911. [PMID: 10026271]
3. Hyland, S.A., Eveland, S.S. and Anderson, M.S. Cloning, expression, and purification of UDP-3-O-acyl-GlcNAc deacetylase from Pseudomonas aeruginosa: a metalloamidase of the lipid A biosynthesis pathway. J. Bacteriol. 179 (1997) 2029-2037. [PMID: 9068651]
4. Wang, W., Maniar, M., Jain, R., Jacobs, J., Trias, J. and Yuan, Z. A fluorescence-based homogeneous assay for measuring activity of UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase. Anal. Biochem. 290 (2001) 338-346. [PMID: 11237337]
5. Whittington, D.A., Rusche, K.M., Shin, H., Fierke, C.A. and Christianson, D.W. Crystal structure of LpxC, a zinc-dependent deacetylase essential for endotoxin biosynthesis. Proc. Natl. Acad. Sci. USA 100 (2003) 8146-8150. [PMID: 12819349]
6. Mochalkin, I., Knafels, J.D. and Lightle, S. Crystal structure of LpxC from Pseudomonas aeruginosa complexed with the potent BB-78485 inhibitor. Protein Sci. 17 (2008) 450-457. [PMID: 18287278]
Accepted name: allantoate deiminase
Reaction: allantoate + H2O = (S)-ureidoglycine + NH3 + CO2
Other name(s): allantoate amidohydrolase
Systematic name: allantoate amidinohydrolase (decarboxylating)
Comments: This enzyme is part of the ureide pathway, which permits certain organisms to recycle the nitrogen in purine compounds. This enzyme, which liberates ammonia from allantoate, is present in plants and bacteria. In plants it is localized in the endoplasmic reticulum. Requires manganese.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 37289-13-7
References:
1. Vogels, G.D. Reversible activation of allantoate amidohydrolase by acid-pretreatment and other properties of the enzyme. Biochim. Biophys. Acta 113 (1966) 277-291. [PMID: 5328936]
2. Serventi, F., Ramazzina, I., Lamberto, I., Puggioni, V., Gatti, R. and Percudani, R. Chemical basis of nitrogen recovery through the ureide pathway: formation and hydrolysis of S-ureidoglycine in plants and bacteria. ACS Chem Biol 5 (2010) 203-214. [PMID: 20038185]
Accepted name: UDP-2,3-diacylglucosamine diphosphatase
Reaction: UDP-2,3-bis[(3R)-3-hydroxymyristoyl]-α-D-glucosamine + H2O = 2,3-bis[(3R)-3-hydroxymyristoyl]-β-D-glucosaminyl 1-phosphate + UMP
Other name(s): UDP-2,3-diacylglucosamine hydrolase; UDP-2,3-diacylglucosamine pyrophosphatase; ybbF (gene name); lpxH (gene name)
Systematic name: UDP-2,3-bis[(3R)-3-hydroxymyristoyl]-α-D-glucosamine 2,3-bis[(3R)-3-hydroxymyristoyl]-β-D-glucosaminyl 1-phosphate phosphohydrolase
Comments: The enzyme catalyses a step in the biosynthesis of lipid A.
References:
1. Babinski, K.J., Ribeiro, A.A. and Raetz, C.R. The Escherichia coli gene encoding the UDP-2,3-diacylglucosamine pyrophosphatase of lipid A biosynthesis. J. Biol. Chem. 277 (2002) 25937-25946. [PMID: 12000770]
2. Babinski, K.J., Kanjilal, S.J. and Raetz, C.R. Accumulation of the lipid A precursor UDP-2,3-diacylglucosamine in an Escherichia coli mutant lacking the lpxH gene. J. Biol. Chem. 277 (2002) 25947-25956. [PMID: 12000771]
Accepted name: 1,4-dihydroxy-2-naphthoyl-CoA synthase
Reaction: o-succinylbenzoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O
For diagram of reaction, click here
Other name(s): naphthoate synthase; 1,4-dihydroxy-2-naphthoate synthase; dihydroxynaphthoate synthase; o-succinylbenzoyl-CoA 1,4-dihydroxy-2-naphthoate-lyase (cyclizing), MenB
Systematic name: o-succinylbenzoyl-CoA dehydratase (cyclizing)
Comments: This enzyme is involved in the synthesis of 1,4-dihydroxy-2-naphthoate, a branch point metabolite leading to the biosynthesis of menaquinone (vitamin K2, in bacteria), phylloquinone (vitamin K1 in plants), and many plant pigments. The coenzyme A group is subsequently removed from the product by an as-yet uncharacterized thioesterase [3].
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 61328-42-5
References:
1. Meganathan, R. and Bentley, R. Menaquinone (vitamin K2) biosynthesis: conversion of o-succinylbenzoic acid to 1,4-dihydroxy-2-naphthoic acid by Mycobacterium phlei enzymes. J. Bacteriol. 140 (1979) 92-98. [PMID: 500558]
2. Kolkmann, R. and Leistner, E. 4-(2'-Carboxyphenyl)-4-oxobutyryl coenzyme A ester, an intermediate in vitamin K2 (menaquinone) biosynthesis. Z. Naturforsch. C: Sci. 42 (1987) 1207-1214. [PMID: 2966501]
3. Johnson, T.W., Shen, G., Zybailov, B., Kolling, D., Reategui, R., Beauparlant, S., Vassiliev, I.R., Bryant, D.A., Jones, A.D., Golbeck, J.H. and Chitnis, P.R. Recruitment of a foreign quinone into the A(1) site of photosystem I. I. Genetic and physiological characterization of phylloquinone biosynthetic pathway mutants in Synechocystis sp. pcc 6803. J. Biol. Chem. 275 (2000) 8523-8530. [PMID: 10722690]
4. Truglio, J.J., Theis, K., Feng, Y., Gajda, R., Machutta, C., Tonge, P.J. and Kisker, C. Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis. J. Biol. Chem. 278 (2003) 42352-42360. [PMID: 12909628]
Accepted name: α-farnesene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (3E,6E)-α-farnesene + diphosphate
Other name(s): (E,E)-α-farnesene synthase; AFS1; MdAFS1
Systematic name: (2E,6E)-farnesyl-diphosphate lyase [(3E,6E)-α-farnesene-forming]
References:
1. Pechous, S.W. and Whitaker, B.D. Cloning and functional expression of an (E,E)-α-farnesene synthase cDNA from peel tissue of apple fruit. Planta 219 (2004) 84-94. [PMID: 14740213]
2. Green, S., Squire, C.J., Nieuwenhuizen, N.J., Baker, E.N. and Laing, W. Defining the potassium binding region in an apple terpene synthase. J. Biol. Chem. 284 (2009) 8661-8669. [PMID: 19181671]
3. Nieuwenhuizen, N.J., Wang, M.Y., Matich, A.J., Green, S.A., Chen, X., Yauk, Y.K., Beuning, L.L., Nagegowda, D.A., Dudareva, N. and Atkinson, R.G. Two terpene synthases are responsible for the major sesquiterpenes emitted from the flowers of kiwifruit (Actinidia deliciosa). J. Exp. Bot. 60 (2009) 3203-3219. [PMID: 19516075]
Accepted name: β-farnesene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (E)-β-farnesene + diphosphate
Other name(s): farnesene synthase; terpene synthase 10; terpene synthase 10-B73; TPS10
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(E)-β-farnesene-forming]
References:
1. Zhao, B., Lei, L., Vassylyev, D.G., Lin, X., Cane, D.E., Kelly, S.L., Yuan, H., Lamb, D.C. and Waterman, M.R. Crystal structure of albaflavenone monooxygenase containing a moonlighting terpene synthase active site. J. Biol. Chem. 284 (2009) 36711-36719. [PMID: 19858213]
2. Picaud, S., Brodelius, M. and Brodelius, P.E. Expression, purification and characterization of recombinant (E)-β-farnesene synthase from Artemisia annua. Phytochemistry 66 (2005) 961-967. [PMID: 15896363]
3. Kollner, T.G., Gershenzon, J. and Degenhardt, J. Molecular and biochemical evolution of maize terpene synthase 10, an enzyme of indirect defense. Phytochemistry 70 (2009) 1139-1145. [PMID: 19646721]
4. Schnee, C., Kollner, T.G., Held, M., Turlings, T.C., Gershenzon, J. and Degenhardt, J. The products of a single maize sesquiterpene synthase form a volatile defense signal that attracts natural enemies of maize herbivores. Proc. Natl. Acad. Sci. USA 103 (2006) 1129-1134. [PMID: 16418295]
5. Maruyama, T., Ito, M. and Honda, G. Molecular cloning, functional expression and characterization of (E)-β farnesene synthase from Citrus junos. Biol. Pharm. Bull. 24 (2001) 1171-1175. [PMID: 11642326]
6. Crock, J., Wildung, M. and Croteau, R. Isolation and bacterial expression of a sesquiterpene synthase cDNA clone from peppermint (Mentha × piperita, L.) that produces the aphid alarm pheromone (E)-β-farnesene. Proc. Natl. Acad. Sci. USA 94 (1997) 12833-12838. [PMID: 9371761]
7. Schnee, C., Kollner, T.G., Gershenzon, J. and Degenhardt, J. The maize gene terpene synthase 1 encodes a sesquiterpene synthase catalyzing the formation of (E)-β-farnesene, (E)-nerolidol, and (E,E)-farnesol after herbivore damage. Plant Physiol. 130 (2002) 2049-2060. [PMID: 12481088]
8. Huber, D.P.W., Philippe, R.N., Godard, K.-A., Sturrock, R.N. and Bohlmann, J. Characterization of four terpene synthase cDNAs from methyl jasmonate-induced Douglas-fir, Pseudotsuga menziesii. Phytochemistry 66 (2005) 1427-1439. [PMID: 15921711]
Accepted name: D-sedoheptulose 7-phosphate isomerase
Reaction: D-sedoheptulose 7-phosphate = D-glycero-D-manno-heptose 7-phosphate
Other name(s): sedoheptulose-7-phosphate isomerase; phosphoheptose isomerase; gmhA (gene name); lpcA (gene name)
Systematic name: D-glycero-D-manno-heptose 7-phosphate aldose-ketose-isomerase
Comments: In Gram-negative bacteria the enzyme is involved in biosynthesis of ADP-L-glycero-β-D-manno-heptose, which is utilized for assembly of the lipopolysaccharide inner core. In Gram-positive bacteria the enzyme is involved in biosynthesis of GDP-D-glycero-α-D-manno-heptose, which is required for assembly of S-layer glycoprotein.
References:
1. Kneidinger, B., Marolda, C., Graninger, M., Zamyatina, A., McArthur, F., Kosma, P., Valvano, M.A. and Messner, P. Biosynthesis pathway of ADP-L-glycero-β-D-manno-heptose in Escherichia coli. J. Bacteriol. 184 (2002) 363-369. [PMID: 11751812]
2. Kneidinger, B., Graninger, M., Puchberger, M., Kosma, P. and Messner, P. Biosynthesis of nucleotide-activated D-glycero-D-manno-heptose. J. Biol. Chem. 276 (2001) 20935-20944. [PMID: 11279237]
3. Valvano, M.A., Messner, P. and Kosma, P. Novel pathways for biosynthesis of nucleotide-activated glycero-manno-heptose precursors of bacterial glycoproteins and cell surface polysaccharides. Microbiology 148 (2002) 1979-1989. [PMID: 12101286]
4. Kim, M.S. and Shin, D.H. A preliminary X-ray study of sedoheptulose-7-phosphate isomerase from Burkholderia pseudomallei. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 65 (2009) 1110-1112. [PMID: 19923728]
5. Taylor, P.L., Blakely, K.M., de Leon, G.P., Walker, J.R., McArthur, F., Evdokimova, E., Zhang, K., Valvano, M.A., Wright, G.D. and Junop, M.S. Structure and function of sedoheptulose-7-phosphate isomerase, a critical enzyme for lipopolysaccharide biosynthesis and a target for antibiotic adjuvants. J. Biol. Chem. 283 (2008) 2835-2845. [PMID: 18056714]
Accepted name: carnosine synthase
Reaction: ATP + L-histidine + β-alanine = ADP + phosphate + carnosine
Glossary: carnosine = N-β-alanyl-L-histidine
Other name(s): carnosine synthetase; carnosine-anserine synthetase; homocarnosine-carnosine synthetase; carnosine-homocarnosine synthetase; L-histidine:β-alanine ligase (AMP-forming) (incorrect)
Systematic name: L-histidine:β-alanine ligase (ADP-forming)
Comments: This enzyme was thought to form AMP [1,2], but studies with highly purified enzyme proved that it forms ADP [4]. Carnosine is a dipeptide that is present at high concentrations in skeletal muscle and the olfactory bulb of vertebrates [3]. It is also found in the skeletal muscle of some invertebrates. The enzyme can also catalyse the formation of homocarnosine from 4-aminobutanoate and L-histidine, with much lower activity [4].
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 9023-61-4
References:
1. Kalyankar, G.D. and Meister, A. Enzymatic synthesis of carnosine and related β-alanyl and γ-aminobutyryl peptides. J. Biol. Chem. 234 (1959) 3210-3218. [PMID: 14404206]
2. Stenesh, J.J. and Winnick, T. Carnosine-anserine synthetase of muscle. 4. Partial purification of the enzyme and further studies of β-alanyl peptide synthesis. Biochem. J. 77 (1960) 575-581. [PMID: 16748858]
3. Crush, K.G. Carnosine and related substances in animal tissues. Comp. Biochem. Physiol. 34 (1970) 3-30. [PMID: 4988625]
4. Drozak, J., Veiga-da-Cunha, M., Vertommen, D., Stroobant, V. and Van Schaftingen, E. Molecular identification of carnosine synthase as ATP-grasp domain-containing protein 1 (ATPGD1). J. Biol. Chem. 285 (2010) 9346-9356. [PMID: 20097752]