An asterisk before "EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: 4-oxoproline reductase
Reaction: cis-4-hydroxy-L-proline + NAD+ = 4-oxo-L-proline + NADH + H+
Other name(s): cis-hydroxy-L-proline oxidase
Systematic name: cis-4-hydroxy-L-proline:NAD+ oxidoreductase (4-oxo-L-proline forming)
Comments: The enzyme, isolated from animals, is specific for 4-oxo-L-proline and cis-4-hydroxy-L-proline. It has no activity with trans-4-hydroxy-L-proline.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37250-37-6
References:
1. Smith, T.E. and Mitoma, C. Partial purification and some properties of 4-ketoproline reductase. J. Biol. Chem. 237 (1962) 1177-1180. [PMID: 13914427]
2. Kwiatkowski, S., Bozko, M., Zarod, M., Witecka, A., Kocdemir, K., Jagielski, A.K. and Drozak, J. Recharacterization of the mammalian cytosolic type 2 (R)-β-hydroxybutyrate dehydrogenase (BDH2) as 4-oxo-L-proline reductase (EC 1.1.1.104). J. Biol. Chem. 298 (2022) 101708. [PMID: 35150746]
Accepted name: D-xylose reductase [NAD(P)H]
Reaction: xylitol + NAD(P)+ = D-xylose + NAD(P)H + H+
Other name(s): XylR; msXR; dsXR; dual specific xylose reductase; NAD(P)H-dependent xylose reductase; xylose reductase (ambiguous); D-xylose reductase (ambiguous)
Systematic name: xylitol:NAD(P)+ oxidoreductase
Comments: Xylose reductases catalyse the reduction of xylose to xylitol, the initial reaction in the fungal D-xylose degradation pathway. Most of the enzymes exhibit a strict requirement for NADPH [cf. EC 1.1.1.431, D-xylose reductase (NADPH)]. However, a few D-xylose reductases, such as those from Neurospora crassa [5], Yamadazyma tenuis [2,3], Scheffersomyces stipitis [1], and the thermophilic fungus Chaetomium thermophilum [4,7], have dual coenzyme specificity, though they still prefer NADPH to NADH. Very rarely the enzyme prefers NADH [cf. EC 1.1.1.430, D-xylose reductase (NADH)].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Verduyn, C., Van Kleef, R., Frank, J., Schreuder, H., Van Dijken, J.P. and Scheffers, W.A. Properties of the NAD(P)H-dependent xylose reductase from the xylose-fermenting yeast Pichia stipitis. Biochem. J. 226 (1985) 669-677. [PMID: 3921014]
2. Neuhauser, W., Haltrich, D., Kulbe, K.D. and Nidetzky, B. NAD(P)H-dependent aldose reductase from the xylose-assimilating yeast Candida tenuis. Isolation, characterization and biochemical properties of the enzyme. Biochem. J. 326 (1997) 683-692. [PMID: 9307017]
3. Hacker, B., Habenicht, A., Kiess, M. and Mattes, R. Xylose utilisation: cloning and characterisation of the xylose reductase from Candida tenuis. Biol. Chem. 380 (1999) 1395-1403. [PMID: 10661866]
4. Hakulinen, N., Turunen, O., Janis, J., Leisola, M. and Rouvinen, J. Three-dimensional structures of thermophilic β-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa. Comparison of twelve xylanases in relation to their thermal stability. Eur. J. Biochem. 270 (2003) 1399-1412. [PMID: 12653995]
5. Woodyer, R., Simurdiak, M., van der Donk, W.A. and Zhao, H. Heterologous expression, purification, and characterization of a highly active xylose reductase from Neurospora crassa. Appl. Environ. Microbiol. 71 (2005) 1642-1647. [PMID: 15746370]
6. Fernandes, S., Tuohy, M.G. and Murray, P.G. Xylose reductase from the thermophilic fungus Talaromyces emersonii: cloning and heterologous expression of the native gene (Texr) and a double mutant (TexrK271R + N273D) with altered coenzyme specificity. J. Biosci. 34 (2009) 881-890. [PMID: 20093741]
7. Quehenberger, J., Reichenbach, T., Baumann, N., Rettenbacher, L., Divne, C. and Spadiut, O. Kinetics and predicted structure of a novel xylose reductase from Chaetomium thermophilum. Int. J. Mol. Sci. 20 (2019) . [PMID: 30621365]
Accepted name: sulfoacetaldehyde reductase (NADPH)
Reaction: isethionate + NADP+ = 2-sulfoacetaldehyde + NADPH + H+
Glossary: isethionate = 2-hydroxyethanesulfonate
2-sulfoacetaldehyde = 2-oxoethanesulfonate
Other name(s): isfD (gene name)
Systematic name: isethionate:NADP+ oxidoreductase
Comments: Catalyses the reaction only in the opposite direction. Involved in taurine degradation. The bacterium Chromohalobacter salexigens strain DSM 3043 possesses two enzymes that catalyse this reaction, a constitutive enzyme (encoded by isfD2) and an inducible enzyme (encoded by isfD). The latter is induced by taurine, and is responsible for most of the activity observed in taurine-grown cells. cf. EC 1.1.1.433, sulfoacetaldehyde reductase (NADH).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Krejcik, Z., Hollemeyer, K., Smits, T.H. and Cook, A.M. Isethionate formation from taurine in Chromohalobacter salexigens: purification of sulfoacetaldehyde reductase. Microbiology 156 (2010) 1547-1555. [PMID: 20133363]
Accepted name: D-xylose reductase (NADH)
Reaction: xylitol + NAD+ = D-xylose + NADH + H+
Other name(s): XYL1 (gene name) (ambiguous)
Systematic name: xylitol:NAD+ oxidoreductase
Comments: Xylose reductases catalyse the reduction of xylose to xylitol, the initial reaction in the fungal D-xylose degradation pathway. Most of the enzymes exhibit a strict requirement for NADPH (cf. EC 1.1.1.431, D-xylose reductase (NADPH)). Some D-xylose reductases have dual coenzyme specificity, though they still prefer NADPH to NADH (cf. EC 1.1.1.307, D-xylose reductase [NAD(P)H]). The enzyme from Candida parapsilosis is a rare example of a xylose reductase that significantly prefers NADH, with Km and Vmax values for NADH being 10-fold lower and 10-fold higher, respectively, than for NADPH.
References:
1. Lee, J.K., Koo, B.S. and Kim, S.Y. Cloning and characterization of the xyl1 gene, encoding an NADH-preferring xylose reductase from Candida parapsilosis, and its functional expression in Candida tropicalis. Appl. Environ. Microbiol. 69 (2003) 6179-6188. [PMID: 14532079]
Accepted name: D-xylose reductase (NADPH)
Reaction: xylitol + NADP+ = D-xylose + NADPH + H+
Other name(s): XYL1 (gene name, ambiguous); xyl1 (gene name, ambiguous); xyrA (gene name); xyrB (gene name)
Systematic name: xylitol:NADP+ oxidoreductase
Comments: Xylose reductases catalyse the reduction of xylose to xylitol, the initial reaction in the fungal D-xylose degradation pathway. Most of the enzymes exhibit a strict requirement for NADPH (e.g. the enzymes from Saccharomyces cerevisiae, Aspergillus niger, Trichoderma reesei, Candida tropicalis, Saitozyma flava, and Candida intermedia). Some D-xylose reductases have dual coenzyme specificity, though they still prefer NADPH to NADH (cf. EC 1.1.1.307, D-xylose reductase [NAD(P)H]). Very rarely the enzyme prefers NADH (cf. EC 1.1.1.430, D-xylose reductase (NADH)).
References:
1. Bolen, P.L. and Detroy, R.W. Induction of NADPH-linked D-xylose reductase and NAD-linked xylitol dehydrogenase activities in Pachysolen tannophilus by D-xylose, L-arabinose, or D-galactose. Biotechnol. Bioeng. 27 (1985) 302-307. [PMID: 18553673]
2. Suzuki, T., Yokoyama, S., Kinoshita, Y., Yamada, H., Hatsu, M., Takamizawa, K. and Kawai, K. Expression of xyrA gene encoding for D-xylose reductase of Candida tropicalis and production of xylitol in Escherichia coli. J. Biosci. Bioeng. 87 (1999) 280-284. [PMID: 16232468]
3. Nidetzky, B., Mayr, P., Hadwiger, P. and Stutz, A.E. Binding energy and specificity in the catalytic mechanism of yeast aldose reductases. Biochem. J. 344 Pt 1 (1999) 101-107. [PMID: 10548539]
4. Mayr, P., Bruggler, K., Kulbe, K.D. and Nidetzky, B. D-Xylose metabolism by Candida intermedia: isolation and characterisation of two forms of aldose reductase with different coenzyme specificities. J. Chromatogr. B Biomed. Sci. Appl. 737 (2000) 195-202. [PMID: 10681056]
5. Sene, L., Felipe, M.G., Silva, S.S. and Vitolo, M. Preliminary kinetic characterization of xylose reductase and xylitol dehydrogenase extracted from Candida guilliermondii FTI 20037 cultivated in sugarcane bagasse hydrolysate for xylitol production. Appl. Biochem. Biotechnol. 91-93 (2001) 671-680. [PMID: 11963895]
6. Jeong, E.Y., Sopher, C., Kim, I.S. and Lee, H. Mutational study of the role of tyrosine-49 in the Saccharomyces cerevisiae xylose reductase. Yeast 18 (2001) 1081-1089. [PMID: 11481678]
7. Chroumpi, T., Peng, M., Aguilar-Pontes, M.V., Muller, A., Wang, M., Yan, J., Lipzen, A., Ng, V., Grigoriev, I.V., Makela, M.R. and de Vries, R.P. Revisiting a ‘simple’ fungal metabolic pathway reveals redundancy, complexity and diversity. Microb. Biotechnol. 14 (2021) 2525-2537. [PMID: 33666344]
8. Terebieniec, A., Chroumpi, T., Dilokpimol, A., Aguilar-Pontes, M.V., Makela, M.R. and de Vries, R.P. Characterization of D-xylose reductase, XyrB, from Aspergillus niger. Biotechnol Rep (Amst) 30 (2021) e00610. [PMID: 33842213]
Accepted name: 6-dehydroglucose reductase
Reaction: D-glucose + NADP+ = 6-dehydro-D-glucose + NADPH + H+
Glossary: quinovose = 6-deoxy-D-glucopyranose
Other name(s): D-glucose 6-dehydrogenase; smoB (gene name); squF (gene name)
Systematic name: D-glucose:NADP+ 6-oxidoreductase
Comments: The enzyme, characterized from alphaproteobacteria, is involved in a D-sulfoquinovose degradation pathway.
References:
1. Sharma, M., Lingford, J.P., Petricevic, M., Snow, A.J.D., Zhang, Y., Jarva, M.A., Mui, J.W., Scott, N.E., Saunders, E.C., Mao, R., Epa, R., da Silva, B.M., Pires, D.E.V., Ascher, D.B., McConville, M.J., Davies, G.J., Williams, S.J. and Goddard-Borger, E.D. Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria. Proc. Natl. Acad. Sci. USA 119 (2022) e2116022119. [PMID: 35074914]
2. Liu, J., Wei, Y., Ma, K., An, J., Liu, X., Liu, Y., Ang, E.L., Zhao, H. and Zhang, Y. Mechanistically diverse pathways for sulfoquinovose degradation in bacteria. ACS Catal. 11 (2021) 14740-14750.
Accepted name: sulfoacetaldehyde reductase (NADH)
Reaction: isethionate + NAD+ = 2-sulfoacetaldehyde + NADH + H+
Glossary: isethionate = 2-hydroxyethanesulfonate
2-sulfoacetaldehyde = 2-oxoethanesulfonate
Other name(s): sarD (gene name); tauF (gene name); sqwF (gene name); BkTauF
Systematic name: isethionate:NAD+ oxidoreductase
Comments: The enzymes from the bacteria Bilophila wadsworthia and Clostridium sp. MSTE9 catalyse the reaction only in the reduction direction. In the bacterium Bifidobacterium kashiwanohense the optimal reaction pH for sulfoacetaldehyde reduction is 7.5, while that for isethionate oxidation is 10.0. cf. EC 1.1.1.313, sulfoacetaldehyde reductase (NADPH).
References:
1. Peck, S.C., Denger, K., Burrichter, A., Irwin, S.M., Balskus, E.P. and Schleheck, D. A glycyl radical enzyme enables hydrogen sulfide production by the human intestinal bacterium Bilophila wadsworthia. Proc. Natl. Acad. Sci. USA 116 (2019) 3171-3176. [PMID: 30718429]
2. Xing, M., Wei, Y., Zhou, Y., Zhang, J., Lin, L., Hu, Y., Hua, G.,, N. Nanjaraj Urs, A., Liu, D., Wang, F., Guo, C., Tong, Y., Li, M., Liu, Y., Ang, E.L., Zhao, H., Yuchi, Z. and Zhang, Y. Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteria. Nat. Commun. 10 (2019) 1609. [PMID: 30962433]
3. Zhou, Y., Wei, Y., Nanjaraj Urs, A.N., Lin, L., Xu, T., Hu, Y., Ang, E.L., Zhao, H., Yuchi, Z. and Zhang, Y. Identification and characterization of a new sulfoacetaldehyde reductase from the human gut bacterium Bifidobacterium kashiwanohense. Biosci Rep 39 (2019) . [PMID: 31123167]
4. Liu, J., Wei, Y., Ma, K., An, J., Liu, X., Liu, Y., Ang, E.L., Zhao, H. and Zhang, Y. Mechanistically diverse pathways for sulfoquinovose degradation in bacteria. ACS Catal. 11 (2021) 14740-14750.
Accepted name: glucoside 3-dehydrogenase (cytochrome c)
Reaction: a D-glucoside + a ferric c-type cytochrome = a 3-dehydro-D-glucoside + a ferrous c-type cytochrome
Other name(s): D-glucoside 3-dehydrogenase (ambiguous); D-aldohexopyranoside dehydrogenase (ambiguous); D-aldohexoside:cytochrome c oxidoreductase; hexopyranoside-cytochrome c oxidoreductase
Systematic name: a D-glucoside:ferric c-type cytochrome 3-oxidoreductase
Comments: This bacterial enzyme acts on D-glucose, D-galactose, D-glucosides and D-galactosides, but the best substrates are disaccharides with a glucose moiety at the non-reducing end. It consists of two subunits, a catalytic subunit that contains an FAD cofactor and an iron-sulfur cluster, and a "hitch-hiker" subunit containing a signal peptide for translocation into the periplasm. A dedicated c-type cytochrome protein serves as an electron acceptor, transferring the electrons from the catalytic subunit to the cell's electron transfer chain. cf. EC 1.1.99.13, glucoside 3-dehydrogenase (acceptor).
References:
1. Hayano, K. and Fukui, S. Purification and properties of 3-ketosucrose-forming enzyme from the cells of Agrobacterium tumefaciens. J. Biol. Chem. 242 (1967) 3665-3672. [PMID: 6038493]
2. Nakamura, L.K. and Tyler, D.D. Induction of D-aldohexoside:cytochrome c oxidoreductase in Agrobacterium tumefaciens. J. Bacteriol. 129 (1977) 830-835. [PMID: 838689]
3. Takeuchi, M., Ninomiya, K., Kawabata, K., Asano, N., Kameda, Y. and Matsui, K. Purification and properties of glucoside 3-dehydrogenase from Flavobacterium saccharophilum. J. Biochem. 100 (1986) 1049-1055. [PMID: 3818559]
4. Takeuchi, M., Asano, N., Kameda, Y. and Matsui, K. Physiological role of glucoside 3-dehydrogenase and cytochrome c551 in the sugar oxidizing system of Flavobacterium saccharophilum. J. Biochem. 103 (1988) 938-943. [PMID: 2844746]
5. Tsugawa, W., Horiuchi, S., Tanaka, M., Wake, H. and Sode, K. Purification of a marine bacterial glucose dehydrogenase from Cytophaga marinoflava and its application for measurement of 1,5-anhydro-D-glucitol. Appl. Biochem. Biotechnol. 56 (1996) 301-310. [PMID: 8984902]
6. Kojima, K., Tsugawa, W. and Sode, K. Cloning and expression of glucose 3-dehydrogenase from Halomonas sp. α-15 in Escherichia coli. Biochem. Biophys. Res. Commun. 282 (2001) 21-27. [PMID: 11263965]
7. Zhang, J.F., Zheng, Y.G., Xue, Y.P. and Shen, Y.C. Purification and characterization of the glucoside 3-dehydrogenase produced by a newly isolated Stenotrophomonas maltrophilia CCTCC M 204024. Appl. Microbiol. Biotechnol. 71 (2006) 638-645. [PMID: 16292530]
8. Zhang, J.F., Chen, W.Q. and Chen, H. Gene cloning and expression of a glucoside 3-dehydrogenase from Sphingobacterium faecium ZJF-D6, and used it to produce N-p-nitrophenyl-3-ketovalidamine. World J. Microbiol. Biotechnol. 33 (2017) 21. [PMID: 28044272]
9. Miyazaki, R., Yamazaki, T., Yoshimatsu, K., Kojima, K., Asano, R., Sode, K. and Tsugawa, W. Elucidation of the intra- and inter-molecular electron transfer pathways of glucoside 3-dehydrogenase. Bioelectrochemistry 122 (2018) 115-122. [PMID: 29625423]
Accepted name: glucoside 3-dehydrogenase (acceptor)
Reaction: sucrose + acceptor = 3-dehydro-α-D-glucosyl-β-D-fructofuranoside + reduced acceptor
Other name(s): D-glucoside 3-dehydrogenase (ambiguous); D-aldohexopyranoside dehydrogenase (ambiguous); D-aldohexoside:(acceptor) 3-oxidoreductase; thuA (gene name); thuB (gene name); glucoside 3-dehydrogenase
Systematic name: D-aldohexoside:acceptor 3-oxidoreductase
Comments: The enzymes from members of the Rhizobiaceae family (such as Agrobacterium tumefaciens) act on disaccharides that contain a glucose moiety at the non-reducing end, such as sucrose, trehalose, leucrose, palatinose, trehalulose, and maltitol, forming the respective 3'-keto derivatives. cf. EC 1.1.2.11, glucoside 3-dehydrogenase (cytochrome c).
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9031-74-7
References:
1. Jensen, J.B., Ampomah, O.Y., Darrah, R., Peters, N.K. and Bhuvaneswari, T.V. Role of trehalose transport and utilization in Sinorhizobium meliloti-alfalfa interactions. Mol. Plant Microbe Interact. 18 (2005) 694-702. [PMID: 16042015]
2. Ampomah, O.Y., Avetisyan, A., Hansen, E., Svenson, J., Huser, T., Jensen, J.B. and Bhuvaneswari, T.V. The thuEFGKAB operon of Rhizobia and Agrobacterium tumefaciens codes for transport of trehalose, maltitol, and isomers of sucrose and their assimilation through the formation of their 3-keto derivatives. J. Bacteriol. 195 (2013) 3797-3807. [PMID: 23772075]
3. Ampomah, O.Y. and Jensen, J.B. The trehalose utilization gene thuA ortholog in Mesorhizobium loti does not influence competitiveness for nodulation on Lotus spp. World J. Microbiol. Biotechnol. 30 (2014) 1129-1134. [PMID: 24142427]
Accepted name: succinate dehydrogenase
Reaction: succinate + a quinone = fumarate + a quinol
For diagram of reaction, click here
Other name(s): succinate dehydrogenase (quinone); succinate dehydrogenase (ubiquinone); succinic dehydrogenase; complex II (ambiguous); succinate dehydrogenase complex; SDH (ambiguous); succinate:ubiquinone oxidoreductase; fumarate reductase (quinol); FRD; menaquinol-fumarate oxidoreductase; succinate dehydrogenase (menaquinone); succinate:menaquinone oxidoreductase; fumarate reductase (menaquinone)
Systematic name: succinate:quinone oxidoreductase
Comments: A complex generally comprising an FAD-containing component that also binds the carboxylate substrate (A subunit), a component that contains three different iron-sulfur centers [2Fe-2S], [4Fe-4S], and [3Fe-4S] (B subunit), and a hydrophobic membrane-anchor component (C, or C and D subunits) that is also the site of the interaction with quinones. The enzyme is found in the inner mitochondrial membrane in eukaryotes and the plasma membrane of bacteria and archaea, with the hydrophilic domain extending into the mitochondrial matrix and the cytoplasm, respectively. Under aerobic conditions the enzyme catalyses succinate oxidation, a key step in the citric acid (TCA) cycle, transferring the electrons to quinones in the membrane, thus linking the TCA cycle with the aerobic respiratory chain (where it is known as complex II). Under anaerobic conditions the enzyme functions as a fumarate reductase, transferring electrons from the quinol pool to fumarate, and participating in anaerobic respiration with fumarate as the terminal electron acceptor. The enzyme interacts with the quinone produced by the organism, such as ubiquinone, menaquinone, caldariellaquinone, thermoplasmaquinone, rhodoquinone etc. Some of the enzymes contain two heme subunits in their membrane anchor subunit. These enzymes catalyse an electrogenic reaction and are thus classified as EC 7.1.1.12, succinate dehydrogenase (electrogenic, proton-motive force generating).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9028-11-9
References:
1. Kita, K., Vibat, C.R., Meinhardt, S., Guest, J.R. and Gennis, R.B. One-step purification from Escherichia coli of complex II (succinate: ubiquinone oxidoreductase) associated with succinate-reducible cytochrome b556. J. Biol. Chem. 264 (1989) 2672-2677. [PMID: 2644269]
2. Van Hellemond, J.J. and Tielens, A.G. Expression and functional properties of fumarate reductase. Biochem. J. 304 (1994) 321-331. [PMID: 7998964]
3. Iverson, T.M., Luna-Chavez, C., Cecchini, G. and Rees, D.C. Structure of the Escherichia coli fumarate reductase respiratory complex. Science 284 (1999) 1961-1966. [PMID: 10373108]
4. Cecchini, G., Schroder, I., Gunsalus, R.P. and Maklashina, E. Succinate dehydrogenase and fumarate reductase from Escherichia coli. Biochim. Biophys. Acta 1553 (2002) 140-157. [PMID: 11803023]
5. Figueroa, P., Leon, G., Elorza, A., Holuigue, L., Araya, A. and Jordana, X. The four subunits of mitochondrial respiratory complex II are encoded by multiple nuclear genes and targeted to mitochondria in Arabidopsis thaliana. Plant Mol. Biol. 50 (2002) 725-734. [PMID: 12374303]
6. Cecchini, G. Function and structure of complex II of the respiratory chain. Annu. Rev. Biochem. 72 (2003) 77-109. [PMID: 14527321]
7. Oyedotun, K.S. and Lemire, B.D. The quaternary structure of the Saccharomyces cerevisiae succinate dehydrogenase. Homology modeling, cofactor docking, and molecular dynamics simulation studies. J. Biol. Chem. 279 (2004) 9424-9431. [PMID: 14672929]
8. Kurokawa, T. and Sakamoto, J. Purification and characterization of succinate:menaquinone oxidoreductase from Corynebacterium glutamicum. Arch. Microbiol. 183 (2005) 317-324. [PMID: 15883782]
9. Iwata, F., Shinjyo, N., Amino, H., Sakamoto, K., Islam, M.K., Tsuji, N. and Kita, K. Change of subunit composition of mitochondrial complex II (succinate-ubiquinone reductase/quinol-fumarate reductase) in Ascaris suum during the migration in the experimental host. Parasitol Int 57 (2008) 54-61. [PMID: 17933581]
[EC 1.3.5.4 Transferred entry: fumarate reductase (quinol), now included in EC 1.3.5.1, succinate dehydrogenase. (EC 1.3.5.4 created 2010, modified 2013, deleted 2022)]
Accepted name: aspartate dehydrogenase
Reaction: L-aspartate + H2O + NAD(P)+ = oxaloacetate + NH3 + NAD(P)H + H+ (overall reaction)
(1a) L-aspartate + NAD(P)+ = 2-iminosuccinate + NAD(P)H + H+
(1b) 2-iminosuccinate + H2O = oxaloacetate + NH3 (spontaneous)
Other name(s): AspDH; NAD-dependent aspartate dehydrogenase; NADH2-dependent aspartate dehydrogenase; NADP+-dependent aspartate dehydrogenase; nadX (gene name); L-aspartate:NAD(P)+ oxidoreductase (deaminating)
Systematic name: L-aspartate:NAD(P)+ oxidoreductase (2-iminosuccinate-forming)
Comments: The enzyme is strictly specific for L-aspartate as substrate. It produces the unstable compound 2-iminosuccinate, which, in the presence of water, hydrolyses spontaneously to form oxaloacetate. The enzyme from some archaea and thermophilic bacteria is likely to transfer 2-iminosuccinate directly to EC 2.5.1.72, quinolinate synthase, preventing its hydrolysis and enabling the de novo biosynthesis of NAD+.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37278-97-0
References:
1. Kretovich, W.L., Kariakina, T.I., Weinova, M.K., Sidelnikova, L.I. and Kazakova, O.W. The synthesis of aspartic acid in Rhizobium lupini bacteroids. Plant Soil 61 (1981) 145-156.
2. Okamura, T., Noda, H., Fukuda, S. and Ohsugi, M. Aspartate dehydrogenase in vitamin B12-producing Klebsiella pneumoniae IFO 13541. J. Nutr. Sci. Vitaminol. 44 (1998) 483-490. [PMID: 9819709]
3. Yang, Z., Savchenko, A., Yakunin, A., Zhang, R., Edwards, A., Arrowsmith, C. and Tong, L. Aspartate dehydrogenase, a novel enzyme identified from structural and functional studies of TM1643. J. Biol. Chem. 278 (2003) 8804-8808. [PMID: 12496312]
4. Yoneda, K., Kawakami, R., Tagashira, Y., Sakuraba, H., Goda, S. and Ohshima, T. The first archaeal L-aspartate dehydrogenase from the hyperthermophile Archaeoglobus fulgidus: gene cloning and enzymological characterization. Biochim. Biophys. Acta 1764 (2006) 1087-1093. [PMID: 16731057]
5. Yoneda, K., Sakuraba, H., Tsuge, H., Katunuma, N. and Ohshima, T. Crystal structure of archaeal highly thermostable L-aspartate dehydrogenase/NAD/citrate ternary complex. FEBS J. 274 (2007) 4315-4325. [PMID: 17651440]
6. Li, Y., Kawakami, N., Ogola, H.J., Ashida, H., Ishikawa, T., Shibata, H. and Sawa, Y. A novel L-aspartate dehydrogenase from the mesophilic bacterium Pseudomonas aeruginosa PAO1: molecular characterization and application for L-aspartate production. Appl. Microbiol. Biotechnol. 90 (2011) 1953-1962. [PMID: 21468714]
7. Li, Y., Ishida, M., Ashida, H., Ishikawa, T., Shibata, H. and Sawa, Y. A non-NadB type L-aspartate dehydrogenase from Ralstonia eutropha strain JMP134: molecular characterization and physiological functions. Biosci. Biotechnol. Biochem. 75 (2011) 1524-1532. [PMID: 21821928]
8. Li, Y., Ogola, H.J. and Sawa, Y. L-aspartate dehydrogenase: features and applications. Appl. Microbiol. Biotechnol. 93 (2012) 503-516. [PMID: 22120624]
Accepted name: secondary-alkyl amine dehydrogenase [NAD(P)+]
Reaction: a secondary-alkyl amine + H2O + NAD(P)+ = a ketone + NH3 + NAD(P)H + H+
Glossary: a secondary-alkyl amine = RCHNH2R'
Other name(s): AmDH (ambiguous); amine dehydrogenase (ambiguous)
Systematic name: secondary-alkyl amine:NAD(P)+ oxidoreductase (deaminating)
Comments: The enzyme has been shown to react preferentially with short-chain ketones such as cyclohexanone, primary amine groups attached to secondary alkyl groups, or D- and L-amino acids. It also reduces aldehydes to primary amines. Cosubstrate preference depends on the substrate.
References:
1. Itoh, N., Yachi, C. and Kudome, T. Determining a novel NAD+-dependent amine dehydrogenase with a broad substrate range from Streptomyces virginiae IFO 12827: purification and characterization. Journal of Molecular Catalysis B: Enzymatic 10 (2000) 281-290.
2. Mayol, O., David, S., Darii, E., Debard, A., Mariage, A., Pellouin, V., Petit, J.L., Salanoubat, M., de Berardinis, V., Zaparucha, A. and Vergne-Vaxelaire, C. Asymmetric reductive amination by a wild-type amine dehydrogenase from the thermophilic bacteria Petrotoga mobilis. Catalysis Science & Technology 6 (2016) 7421-7428.
3. Mayol, O., Bastard, K., Beloti, L., Frese, A., Turkenburg, J.P., Petit, J.L., Mariage, A., Debard, A., Pellouin, V., Perret, A., de Berardinis, V., Zaparucha, A., Grogan, G. and Vergne-Vaxelaire, C. A family of native amine dehydrogenases for the asymmetric reductive amination of ketones. Nature Catalysis 2 (2019) 324-333.
4. Lee, S., Jeon, H., Giri, P., Lee, U.J., Jung, H., Lim, S., Sarak, S., Khobragade, T.P., Kim, B.G. and Yun, H. The reductive amination of carbonyl compounds using native amine dehydrogenase from Laribacter hongkongensis. Biotechnol. Bioprocess Eng. 26 (2021) 384-391.
Accepted name: dimethylglycine oxidase
Reaction: N,N-dimethylglycine + 5,6,7,8-tetrahydrofolate + O2 = sarcosine + 5,10-methylenetetrahydrofolate + H2O2
Other name(s): dmg (gene name); N,N-dimethylglycine:oxygen oxidoreductase (demethylating)
Systematic name: N,N-dimethylglycine,5,6,7,8-tetrahydrofolate:oxygen oxidoreductase (demethylating,5,10-methylenetetrahydrofolate-forming)
Comments: A flavoprotein (FAD). The enzyme, characterized from the bacterium Arthrobacter globiformis, contains two active sites connected by a large "reaction chamber". An imine intermediate is transferred between the sites, eliminating the production of toxic formaldehyde. In the absence of folate the enzyme does form formaldehyde. Does not oxidize sarcosine. cf. EC 1.5.8.4, dimethylglycine dehydrogenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37256-30-7
References:
1. Mori, N., Kawakami, B., Tani, Y. and Yamada, H. Purification and properties of dimethylglycine oxidase from Cylindrocarpon didymum M-1. Agric. Biol. Chem. 44 (1980) 1383-1389.
2. Meskys, R., Harris, R.J., Casaite, V., Basran, J. and Scrutton, N.S. Organization of the genes involved in dimethylglycine and sarcosine degradation in Arthrobacter spp.: implications for glycine betaine catabolism. Eur. J. Biochem. 268 (2001) 3390-3398. [PMID: 11422368]
3. Basran, J., Bhanji, N., Basran, A., Nietlispach, D., Mistry, S., Meskys, R. and Scrutton, N.S. Mechanistic aspects of the covalent flavoprotein dimethylglycine oxidase of Arthrobacter globiformis studied by stopped-flow spectrophotometry. Biochemistry 41 (2002) 4733-4743. [PMID: 11926836]
4. Leys, D., Basran, J. and Scrutton, N.S. Channelling and formation of ‘active’ formaldehyde in dimethylglycine oxidase. EMBO J. 22 (2003) 4038-4048. [PMID: 12912903]
5. Basran, J., Fullerton, S., Leys, D. and Scrutton, N.S. Mechanism of FAD reduction and role of active site residues His-225 and Tyr-259 in Arthrobacter globiformis dimethylglycine oxidase: analysis of mutant structure and catalytic function. Biochemistry 45 (2006) 11151-11161. [PMID: 16964976]
6. Tralau, T., Lafite, P., Levy, C., Combe, J.P., Scrutton, N.S. and Leys, D. An internal reaction chamber in dimethylglycine oxidase provides efficient protection from exposure to toxic formaldehyde. J. Biol. Chem. 284 (2009) 17826-17834. [PMID: 19369258]
7. Casaite, V., Poviloniene, S., Meskiene, R., Rutkiene, R. and Meskys, R. Studies of dimethylglycine oxidase isoenzymes in Arthrobacter globiformis cells. Curr. Microbiol. 62 (2011) 1267-1273. [PMID: 21188587]
Accepted name: fructosyl amine oxidase (glucosone-forming)
Reaction: an N-(1-deoxy-D-fructos-1-yl)amine + O2 + H2O = D-glucosone + an amine + H2O2 (overall reaction)
(1a) an N-(1-deoxy-D-fructos-1-yl)amine + O2 = a 2-[(3S,4R,5R)-3,4,5,6-tetrahydroxy-2-oxohexylidene]amine + H2O2
(1b) a 2-[(3S,4R,5R)-3,4,5,6-tetrahydroxy-2-oxohexylidene]amine + H2O = D-glucosone + an amine (spontaneous)
Other name(s): amadoriase
Systematic name: N-(1-deoxy-D-fructos-1-yl)amine:oxygen 2-oxidoreductase (glucosone-forming)
Comments: Reducing sugars such as glucose react with amino groups in proteins via the spontaeous Maillard reaction, forming an unstable product that undergoes spontaneous rearrangement to a keto amine compound. These reactions are known as glycation reactions, and the stable products are known as Amadori products. This enzyme, which contains an FAD cofactor, catalyses a deglycation reaction that regenerates the amine reactant. By-products are glucosone and hydrogen peroxide. The enzymes have been reported from fungi and bacteria, but not from higher eukaryotes. Specific enzymes differ in their substrate specificity. cf. EC 1.5.3.26, fructosyl amine oxidase (fructosamine-forming).
References:
1. Horiuchi, T., Kurokawa, T. and Saito, N. Purification and properties of fructosyl-amino acid oxidase from Corynebacterium sp. 2-4-1. Agr Biol Chem Tokyo 53 (1989) 103-110.
2. Takahashi, M., Pischetsrieder, M. and Monnier, V.M. Molecular cloning and expression of amadoriase isoenzyme (fructosyl amine:oxygen oxidoreductase, EC 1.5.3) from Aspergillus fumigatus. J. Biol. Chem. 272 (1997) 12505-12507. [PMID: 9139700]
3. Hirokawa, K. and Kajiyama, N. Recombinant agrobacterium AgaE-like protein with fructosyl amino acid oxidase activity. Biosci. Biotechnol. Biochem. 66 (2002) 2323-2329. [PMID: 12506967]
4. Wu, X. and Monnier, V.M. Enzymatic deglycation of proteins. Arch. Biochem. Biophys. 419 (2003) 16-24. [PMID: 14568004]
5. Sakaue, R., Nakatsu, T., Yamaguchi, Y., Kato, H. and Kajiyama, N. Crystallization and preliminary crystallographic analysis of bacterial fructosyl amino acid oxidase. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 61 (2005) 196-198. [PMID: 16510992]
Accepted name: fructosyl amine oxidase (fructosamine-forming)
Reaction: an N-(1-deoxy-D-fructos-1-yl)amine + O2 + H2O = (1-deoxy-D-fructos-1-yl)amine + an aldehyde + H2O2
Systematic name: N-(1-deoxy-D-fructos-1-yl)amine:oxygen oxidoreductase (fructosamine-forming)
Comments: Reducing sugars such as glucose react with amino groups in proteins via the spontaeous Maillard reaction, forming an unstable product that undergoes spontaneous rearrangement to a keto amine compound. These reactions are known as glycation reactions, and the stable products are known as Amadori products. This enzyme, characterized from a Pseudomonas sp. strain, cleaves the Amadori products at the alkylamine bond. All other known fructosyl amine oxidases cleave the ketoamine bond (cf. EC 1.5.3.25, fructosyl amine oxidase (glucosone-forming)).
References:
1. Gerhardinger, C., Marion, M.S., Rovner, A., Glomb, M. and Monnier, V.M. Novel degradation pathway of glycated amino acids into free fructosamine by a Pseudomonas sp. soil strain extract. J. Biol. Chem. 270 (1995) 218-224. [PMID: 7814378]
2. Saxena, A.K., Saxena, P. and Monnier, V.M. Purification and characterization of a membrane-bound deglycating enzyme (1-deoxyfructosyl alkyl amino acid oxidase, EC 1.5.3) from a Pseudomonas sp. soil strain. J. Biol. Chem. 271 (1996) 32803-32809. [PMID: 8955117]
3. Wu, X. and Monnier, V.M. Enzymatic deglycation of proteins. Arch. Biochem. Biophys. 419 (2003) 16-24. [PMID: 14568004]
Accepted name: N,N-dimethylglycine/sarcosine dehydrogenase (ferredoxin)
Reaction: (1) N,N-dimethylglycine + 2 oxidized ferredoxin + H2O = sarcosine + formaldehyde + 2 reduced ferredoxin + 2 H+
(2) sarcosine + 2 oxidized ferredoxin + H2O = glycine + formaldehyde + 2 reduced ferredoxin + 2 H+
Other name(s): ddhC (gene name); dgcA (gene name)
Systematic name: N,N-dimethylglycine/sarcosine:ferredoxin oxidoreductase (demethylating)
Comments: This bacterial enzyme is involved in degradation of glycine betaine. The enzyme contains non-covalently bound FAD and NAD(P) cofactors, and catalyses the demethylation of both N,N-dimethylglycine and sarcosine, releasing formaldehyde and forming glycine as the final product. The enzyme can utilize both NAD+ and NADP+, but the catalytic efficiency with NAD+ is ~5-fold higher. The native electron acceptor of the enzyme is a membrane-bound clostridial-type ferredoxin, which transfers the electrons to an electron-transfer flavoprotein (ETF).
References:
1. Wargo, M.J., Szwergold, B.S. and Hogan, D.A. Identification of two gene clusters and a transcriptional regulator required for Pseudomonas aeruginosa glycine betaine catabolism. J. Bacteriol. 190 (2008) 2690-2699. [PMID: 17951379]
2. Yang, T., Shao, Y.H., Guo, L.Z., Meng, X.L., Yu, H. and Lu, W.D. Role of N,N-dimethylglycine and its catabolism to sarcosine in Chromohalobacter salexigens DSM 3043. Appl. Environ. Microbiol. 86 (2020) . [PMID: 32631860]
[EC 1.8.1.3 Deleted entry: hypotaurine dehydrogenase. The reaction is now known to be catalyzed by EC 1.14.13.8, flavin-containing monooxygenase. (EC 1.8.1.3 created 1972, deleted 2022)]
Accepted name: 2-oxoadipate dioxygenase/decarboxylase
Reaction: 2-oxoadipate + O2 = (R)-2-hydroxyglutarate + CO2
Other name(s): ydcJ (gene name)
Systematic name: 2-oxoadipate dioxygenase/carboxy lyase
Comments: The enzyme, characterized from the bacterium Pseudomonas putida, is involved in an L-lysine catabolic pathway. Contains Fe(II).
References:
1. Thompson, M.G., Blake-Hedges, J.M., Cruz-Morales, P., Barajas, J.F., Curran, S.C., Eiben, C.B., Harris, N.C., Benites, V.T., Gin, J.W., Sharpless, W.A., Twigg, F.F., Skyrud, W., Krishna, R.N., Pereira, J.H., Baidoo, E.EK., Petzold, C.J., Adams, P.D., Arkin, A.P., Deutschbauer, A.M. and Keasling, J.D. Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism. mBio 10 (2019) . [PMID: 31064836]
Accepted name: (R)-3-[(carboxymethyl)amino]fatty acid dioxygenase/decarboxylase
Reaction: a (3R)-3-[(carboxylmethyl)amino]fatty acid + 2 2-oxoglutarate + 2 O2 = a (3R)-3-isocyanyl-fatty acid + 2 succinate + 3 CO2 + 2 H2O (overall reaction)
(1a) a (3R)-3-[(carboxylmethyl)amino]fatty acid + 2-oxoglutarate + O2 = a (3R)-3-{[carboxy(hydroxy)methyl]amino}fatty acid + succinate + CO2
(1b) a (3R)-3-{[carboxy(hydroxy)methyl]amino}fatty acid + 2-oxoglutarate + O2 = a (3R)-3-isocyanyl-fatty acid + succinate + 2 CO2 + 2 H2O
Other name(s): scoE (gene name); mmaE (gene name); Rv0097 (locus name)
Systematic name: (3R)-3-[(carboxylmethyl)amino]fatty acid,2-oxoglutarate:oxygen oxidoreductase (isonitrile-forming)
Comments: Requires Fe(II). The enzyme, found in actinobacterial species, participates in the biosynthesis of isonitrile-containing lipopeptides. The reaction comprises two catalytic cycles, each consuming an oxygen molecule and a 2-oxoglutarate molecule. In the first cycle the substrate is hydroxylated, while in the second cycle the enzyme catalyses a decarboxylation/oxidation reaction that produces an isonitrile group.
References:
1. Harris, N.C., Sato, M., Herman, N.A., Twigg, F., Cai, W., Liu, J., Zhu, X., Downey, J., Khalaf, R., Martin, J., Koshino, H. and Zhang, W. Biosynthesis of isonitrile lipopeptides by conserved nonribosomal peptide synthetase gene clusters in Actinobacteria. Proc. Natl. Acad. Sci. USA 114 (2017) 7025-7030. [PMID: 28634299]
2. Harris, N.C., Born, D.A., Cai, W., Huang, Y., Martin, J., Khalaf, R., Drennan, C.L. and Zhang, W. Isonitrile formation by a non-heme iron(II)-dependent oxidase/decarboxylase. Angew. Chem. Int. Ed. Engl. 57 (2018) 9707-9710. [PMID: 29906336]
3. Jonnalagadda, R., Del Rio Flores, A., Cai, W., Mehmood, R., Narayanamoorthy, M., Ren, C., Zaragoza, J.PT., Kulik, H.J., Zhang, W. and Drennan, C.L. Biochemical and crystallographic investigations into isonitrile formation by a nonheme iron-dependent oxidase/decarboxylase. J. Biol. Chem. 296 (2021) 100231. [PMID: 33361191]
Accepted name: protein-L-histidine (3S)-3-hydroxylase
Reaction: a [protein]-L-histidine + 2-oxoglutarate + O2 = a [protein]-(3S)-3-hydroxy-L-histidine + succinate + CO2
Other name(s): RIOX1 (gene name); RIOX2 (gene name); protein histidyl hydroxylase
Systematic name: protein-L-histidine,2-oxoglutarate:oxygen oxidoreductase (3S-hydroxylating)
Comments: The human enzymes encoded by the RIOX1 and RIOX2 genes catalyse the hydroxylation of L-histidine residues in the 60S ribosomal proteins Rpl8 and L27a, respectively. Both proteins contain JmjC and winged helix domains, and both also catalyse histone L-lysine demethylation activities.
References:
1. Ge, W., Wolf, A., Feng, T., Ho, C.H., Sekirnik, R., Zayer, A., Granatino, N., Cockman, M.E., Loenarz, C., Loik, N.D., Hardy, A.P., Claridge, T.DW., Hamed, R.B., Chowdhury, R., Gong, L., Robinson, C.V., Trudgian, D.C., Jiang, M., Mackeen, M.M., Mccullagh, J.S., Gordiyenko, Y., Thalhammer, A., Yamamoto, A., Yang, M., Liu-Yi, P., Zhang, Z., Schmidt-Zachmann, M., Kessler, B.M., Ratcliffe, P.J., Preston, G.M., Coleman, M.L. and Schofield, C.J. Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans. Nat. Chem. Biol. 8 (2012) 960-962. [PMID: 23103944]
2. Bundred, J.R., Hendrix, E. and Coleman, M.L. The emerging roles of ribosomal histidyl hydroxylases in cell biology, physiology and disease. Cell. Mol. Life Sci. 75 (2018) 4093-4105. [PMID: 30151692]
[EC 1.14.13.147 Transferred entry: taxoid 7β-hydroxylase. Now EC 1.14.14.182, taxoid 7β-hydroxylase (EC 1.14.13.147 created 2012, deleted 2022)]
Accepted name: glycine betaine monooxygenase
Reaction: glycine betaine + NADH + H+ + O2 = N,N-dimethylglycine + formaldehyde + NAD+ + H2O
Other name(s): glycine betaine dioxygenase (incorrect); bmoAB (gene names); gbcAB (gene names)
Systematic name: glycine betaine,NADH:oxygen oxidoreductase (demethylating)
Comments: The enzyme, characterized from the bacteria Pseudomonas aeruginosa and Chromohalobacter salexigens, is involved in a degradation pathway of glycine betaine. It is composed of two subunits - a ferredoxin reductase component that contains FAD, and a terminal oxygenase component that contains a [2Fe-2S] Rieske-type iron-sulfur cluster and a nonheme iron centre.
References:
1. Wargo, M.J., Szwergold, B.S. and Hogan, D.A. Identification of two gene clusters and a transcriptional regulator required for Pseudomonas aeruginosa glycine betaine catabolism. J. Bacteriol. 190 (2008) 2690-2699. [PMID: 17951379]
2. Li, S., Yu, X. and Beattie, G.A. Glycine betaine catabolism contributes to Pseudomonas syringae tolerance to hyperosmotic stress by relieving betaine-mediated suppression of compatible solute synthesis. J. Bacteriol. 195 (2013) 2415-2423. [PMID: 23524610]
3. Shao, Y.H., Guo, L.Z., Zhang, Y.Q., Yu, H., Zhao, B.S., Pang, H.Q. and Lu, W.D. Glycine betaine monooxygenase, an unusual Rieske-type oxygenase system, catalyzes the oxidative N-demethylation of glycine betaine in Chromohalobacter salexigens DSM 3043. Appl. Environ. Microbiol. 84 (2018) . [PMID: 29703733]
Accepted name: brassinosteroid 6-oxygenase
Reaction: 6-deoxocastasterone + 2 O2 + 2 [reduced NADPH—hemoprotein reductase] = castasterone + 3 H2O + 2 [oxidized NADPH—hemoprotein reductase] (overall reaction)
(1a) 6-deoxocastasterone + O2 + [reduced NADPH—hemoprotein reductase] = 6α-hydroxy-6-deoxocastasterone + H2O + [oxidized NADPH—hemoprotein reductase]
(1b) 6α-hydroxy-6-deoxocastasterone + O2 + [reduced NADPH—hemoprotein reductase] = castasterone + 2 H2O + [oxidized NADPH—hemoprotein reductase]
For diagram of reaction, click here
Other name(s): CYP85A1 (gene name); CYP85A2 (gene name); brassinosteroid 6-oxidase
Systematic name: 6-deoxocastasterone,NADPH—hemoprotein reductase:oxygen 6-oxidoreductase (castasteron-forming)
Comments: This cytochrome P-450 (heme thiolate) plant enzyme catalyses the C-6 hydoxylation of several brassinosteroid biosynthesis intermediates, and the further oxidation of the hydroxyl group to an oxo group. Substrates include 6-deoxocastasterone, 6-deoxotyphasterol, 3-dehydro-6-deoxoteasterone, and 6-deoxoteasterone. The CYP85A2 isozyme of Arabidopsis thaliana (but not the CYP85A1 isozyme) also catalyses the activity of EC 1.14.14.180, brassinolide synthase.
References:
1. Shimada, Y., Fujioka, S., Miyauchi, N., Kushiro, M., Takatsuto, S., Nomura, T., Yokota, T., Kamiya, Y., Bishop, G.J. and Yoshida, S. Brassinosteroid-6-oxidases from Arabidopsis and tomato catalyze multiple C-6 oxidations in brassinosteroid biosynthesis. Plant Physiol. 126 (2001) 770-779. [PMID: 11402205]
2. Perez-Espana, V.H., Sanchez-Leon, N. and Vielle-Calzada, J.P. CYP85A1 is required for the initiation of female gametogenesis in Arabidopsis thaliana. Plant Signal Behav. 6 (2011) 321-326. [PMID: 21364326]
Accepted name: brassinolide synthase
Reaction: castasterone + O2 + [reduced NADPH—hemoprotein reductase] = brassinolide + 2 H2O + [oxidized NADPH—hemoprotein reductase]
For diagram of reaction, click here
Other name(s): CYP85A2 (gene name); CYP85A3 (gene name)
Systematic name: castasterone,NADPH—hemoprotein reductase:oxygen oxidoreductase (lactonizing, brassinolide-forming)
Comments: This cytochrome P-450 (heme thiolate) plant enzyme catalyses the latonization of several brassinosteroids, including castasterone, teasterone, and typhasterol. The CYP85A2 enzyme of Arabidopsis thaliana also catalyses the activity of EC 1.14.14.179, brassinosteroid 6-oxygenase.
References:
1. Nomura, T., Kushiro, T., Yokota, T., Kamiya, Y., Bishop, G.J. and Yamaguchi, S. The last reaction producing brassinolide is catalyzed by cytochrome P-450s, CYP85A3 in tomato and CYP85A2 in Arabidopsis. J. Biol. Chem. 280 (2005) 17873-17879. [PMID: 15710611]
2. Kim, T.W., Hwang, J.Y., Kim, Y.S., Joo, S.H., Chang, S.C., Lee, J.S., Takatsuto, S. and Kim, S.K. Arabidopsis CYP85A2, a cytochrome P450, mediates the Baeyer-Villiger oxidation of castasterone to brassinolide in brassinosteroid biosynthesis. Plant Cell 17 (2005) 2397-2412. [PMID: 16024588]
3. Katsumata, T., Hasegawa, A., Fujiwara, T., Komatsu, T., Notomi, M., Abe, H., Natsume, M. and Kawaide, H. Arabidopsis CYP85A2 catalyzes lactonization reactions in the biosynthesis of 2-deoxy-7-oxalactone brassinosteroids. Biosci. Biotechnol. Biochem. 72 (2008) 2110-2117. [PMID: 18685225]
Accepted name: sulfoquinovose monooxygenase
Reaction: 6-sulfo-D-quinovose + FMNH2 + O2 = 6-dehydro-D-glucose + FMN + sulfite + H2O
Glossary: D-quinovose = 6-deoxy-D-glucopyranose
6-dehydro-D-glucose = 6-oxo-D-quinovose
Other name(s): 6-deoxy-6-sulfo-D-glucose monooxygenase; smoC (gene name); squD (gene name)
Systematic name: 6-sulfo-D-quinovose,FMNH2:oxygen oxidoreductase
Comments: The enzyme, characterized from the bacteria Agrobacterium fabrum and Rhizobium oryzae, is involved in a D-sulfoquinovose degradation pathway. FMNH2 is provided by an associated FMN reductase [SmoA, EC 1.5.1.42, FMN reductase (NADH)]..
References:
1. Liu, J., Wei, Y., Ma, K., An, J., Liu, X., Liu, Y., Ang, E.L., Zhao, H. and Zhang, Y. Mechanistically diverse pathways for sulfoquinovose degradation in bacteria. ACS Catal. 11 (2021) 14740-14750.
2. Sharma, M., Lingford, J.P., Petricevic, M., Snow, A.JD., Zhang, Y., Jarva, M.A., Mui, J.W., Scott, N.E., Saunders, E.C., Mao, R., Epa, R., da Silva, B.M., Pires, D.EV., Ascher, D.B., McConville, M.J., Davies, G.J., Williams, S.J. and Goddard-Borger, E.D. Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria. Proc. Natl. Acad. Sci. USA 119 (2022) . [PMID: 35074914]
Accepted name: taxoid 7β-hydroxylase
Reaction: (1) taxusin + [reduced NADPH—hemoprotein reductase] + O2 = 7β-hydroxytaxusin + [oxidized NADPH—hemoprotein reductase] + H2O
(2) 2α-hydroxytaxusin + [reduced NADPH—hemoprotein reductase] + O2 = 2α,7β-dihydroxytaxusin + [oxidized NADPH—hemoprotein reductase] + H2O
Glossary: taxusin = taxa-4(20),11-diene-5α,9α,10β,13α-tetrayl tetraacetate
Systematic name: taxusin, [reduced NADPH—hemoprotein reductase]:oxygen 7-oxidoreductase
Comments: A cytochrome P-450 (heme-thiolate) protein from the yew tree Taxus cuspidata. Does not act on earlier intermediates in taxol biosynthesis.
References:
1. Chau, M., Jennewein, S., Walker, K. and Croteau, R. Taxol biosynthesis: Molecular cloning and characterization of a cytochrome P450 taxoid 7β-hydroxylase. Chem. Biol. 11 (2004) 663-672. [PMID: 15157877]
2. Chau, M. and Croteau, R. Molecular cloning and characterization of a cytochrome P450 taxoid 2α-hydroxylase involved in taxol biosynthesis. Arch. Biochem. Biophys. 427 (2004) 48-57. [PMID: 15178487]
Accepted name: taxoid 2α-hydroxylase
Reaction: (1) taxusin + [reduced NADPH—hemoprotein reductase] + O2 = 2α-hydroxytaxusin + [oxidized NADPH—hemoprotein reductase] + H2O
(2) 7β-hydroxytaxusin + [reduced NADPH—hemoprotein reductase] + O2 = 2α,7β-dihydroxytaxusin + [oxidized NADPH—hemoprotein reductase] + H2O
Glossary: taxusin = taxa-4(20),11-diene-5α,9α,10β,13α-tetrayl tetraacetate
Systematic name: taxusin, [reduced NADPH—hemoprotein reductase]:oxygen 2-oxidoreductase
Comments: A cytochrome P-450 (heme-thiolate) protein from the yew tree Taxus cuspidata. Does not act on earlier intermediates in taxol biosynthesis.
References:
1. Chau, M., Jennewein, S., Walker, K. and Croteau, R. Taxol biosynthesis: Molecular cloning and characterization of a cytochrome P450 taxoid 7β-hydroxylase. Chem. Biol. 11 (2004) 663-672. [PMID: 15157877]
2. Chau, M. and Croteau, R. Molecular cloning and characterization of a cytochrome P450 taxoid 2α-hydroxylase involved in taxol biosynthesis. Arch. Biochem. Biophys. 427 (2004) 48-57. [PMID: 15178487]
[EC 1.14.99.51 Transferred entry: hercynylcysteine S-oxide synthase, now listed as EC 1.21.3.10
, hercynylcysteine S-oxide synthase. (EC 1.14.99.51 created 2015, deleted 2021)]
Accepted name: hercynylcysteine S-oxide synthase
Reaction: hercynine + L-cysteine + O2 = S-(hercyn-2-yl)-L-cysteine S-oxide + H2O
For diagram of reaction click here
Glossary: hercynine = Nα,Nα,Nα-trimethyl-L-histidine
Other name(s): Egt1; Egt-1
Systematic name: hercynine,L-cysteine:oxygen [S-(hercyn-2-yl)-L-cysteine S-oxide-forming]
Comments: Requires Fe2+ for activity. The enzyme, found in fungal species, is part of a fusion protein that also has the the activity of EC 2.1.1.44, L-histidine Nα-methyltransferase. It is part of the biosynthesis pathway of ergothioneine. The enzyme can also use L-selenocysteine to produce hercynylselenocysteine, which can be converted to selenoneine.
References:
1. Pluskal, T., Ueno, M. and Yanagida, M. Genetic and metabolomic dissection of the ergothioneine and selenoneine biosynthetic pathway in the fission yeast, S. pombe, and construction of an overproduction system. PLoS One 9 (2014) e97774. [PMID: 24828577]
Accepted name: methoxylated aromatic compound—corrinoid protein Co-methyltransferase
Reaction: a methoxylated aromatic compound + a [Co(I) methoxylated-aromatic-compound-specific corrinoid protein] = a [methyl-Co(III) methoxylated-aromatic-compound-specific corrinoid protein] + a phenol
Other name(s): mtoB (gene name); mtvB (gene name); vdmB (gene name)
Systematic name: methoxylated aromatic compound:cobamide Co-methyltransferase
Comments: This entry stands for a family of enzymes that have been characterized from acetogenic bacteria and archaeal species. Different members of this family have different substrate specificity. In the methanogenic archaeon Methermicoccus shengliensis the enzyme participates in methanogenesis from methoxylated aromatic compounds, while in acetogenic bacteria and in non-methanogenic archaea it participates in methoxydotrophic growth. Most of the enzymes have a wide specificity and were shown to act on a large number of methoxylated aromatic compounds, carrying a methoxy group at positions 2, 3 or 4 of the aromatic ring. Methylation of the corrinoid protein requires the central cobalt to be in the Co(I) state; during methylation the cobalt is oxidized to the Co(III) state.
References:
1. Kaufmann, F., Wohlfarth, G. and Diekert, G. O-demethylase from Acetobacterium dehalogenans—substrate specificity and function of the participating proteins. Eur. J. Biochem. 253 (1998) 706-711. [PMID: 9654069]
2. Engelmann, T., Kaufmann, F. and Diekert, G. Isolation and characterization of a veratrol:corrinoid protein methyl transferase from Acetobacterium dehalogenans. Arch. Microbiol. 175 (2001) 376-383. [PMID: 11409548]
3. Naidu, D. and Ragsdale, S.W. Characterization of a three-component vanillate O-demethylase from Moorella thermoacetica. J. Bacteriol. 183 (2001) 3276-3281. [PMID: 11344134]
4. Pierce, E., Xie, G., Barabote, R.D., Saunders, E., Han, C.S., Detter, J.C., Richardson, P., Brettin, T.S., Das, A., Ljungdahl, L.G. and Ragsdale, S.W. The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ. Microbiol. 10 (2008) 2550-2573. [PMID: 18631365]
5. Kurth, J.M., Nobu, M.K., Tamaki, H., de Jonge, N., Berger, S., Jetten, M.SM., Yamamoto, K., Mayumi, D., Sakata, S., Bai, L., Cheng, L., Nielsen, J.L., Kamagata, Y., Wagner, T. and Welte, C.U. Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds. ISME J. 15 (2021) 3549-3565. [PMID: 34145392]
6. Welte, C.U., de Graaf, R., Dalcin Martins, P., Jansen, R.S., Jetten, M.SM. and Kurth, J.M. A novel methoxydotrophic metabolism discovered in the hyperthermophilic archaeon Archaeoglobus fulgidus. Environ. Microbiol. 23 (2021) 4017-4033. [PMID: 33913565]
Accepted name: [methyl-Co(III) methoxylated-aromatic-compound-specific corrinoid protein]—tetrahydromethanopterin methyltransferase
Reaction: [a methyl-Co(III) methoxylated-aromatic-compound-specific corrinoid protein] + tetrahydromethanopterin = N5-methyltetrahydromethanopterin + a [Co(I) methoxylated-aromatic-compound-specific corrinoid protein]
Other name(s): mtoA (gene name)
Systematic name: [methylated methoxylated-aromatic-compound-specific corrinoid protein]:tetrahydromethanopterin methyltransferase
Comments: The enzyme has been characterized from several archaeal species. In the methanogenic archaeon Methermicoccus shengliensis the enzyme participates in methanogenesis from methoxylated aromatic compounds, while in the non-methanogenic Archaeoglobus fulgidus it participates in methoxydotrophic growth. The enzyme catalyses the transfer of a methyl group bound to the cobalt cofactor of a dedicated corrinoid protein (MtoC) to tetrahydromethanopterin or tetrahydrosarcinapterin. cf. EC 2.1.1.385, [methyl-Co(III) methoxylated-aromatic-compound-specific corrinoid protein]—tetrahydrofolate methyltransferase.
References:
1. Kurth, J.M., Nobu, M.K., Tamaki, H., de Jonge, N., Berger, S., Jetten, M.SM., Yamamoto, K., Mayumi, D., Sakata, S., Bai, L., Cheng, L., Nielsen, J.L., Kamagata, Y., Wagner, T. and Welte, C.U. Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds. ISME J. (2021) 3549-3565.
2. Welte, C.U., de Graaf, R., Dalcin Martins, P., Jansen, R.S., Jetten, M.SM. and Kurth, J.M. A novel methoxydotrophic metabolism discovered in the hyperthermophilic archaeon Archaeoglobus fulgidus. Environ. Microbiol. (2021) .
Accepted name: [methyl-Co(III) methoxylated-aromatic-compound-specific corrinoid protein]—tetrahydrofolate methyltransferase
Reaction: [a methyl-Co(III) methoxylated-aromatic-compound-specific corrinoid protein] + tetrahydrofolate = N5-methyltetrahydrofolate + a [Co(I) methoxylated-aromatic-compound-specific corrinoid protein]
Other name(s): mtvA (gene name)
Systematic name: [methylated methoxylated-aromatic-compound-specific corrinoid protein]:tetrahydrofolaten methyltransferase
Comments: The enzyme, found in acetogenic bacteria, participates in a pathway for the degradation of methoxylated aromatic compounds (methoxydotrophic growth). The enzyme catalyses the transfer of a methyl group bound to the cobalt cofactor of a dedicated corrinoid protein (MtvC) to tetrahydrofolate. cf. EC 2.1.1.384, [methyl-Co(III) methoxylated-aromatic-compound-specific corrinoid protein]—tetrahydromethanopterin methyltransferase.
References:
1. Kaufmann, F., Wohlfarth, G. and Diekert, G. O-demethylase from Acetobacterium dehalogenans—substrate specificity and function of the participating proteins. Eur. J. Biochem. 253 (1998) 706-711. [PMID: 9654069]
2. Naidu, D. and Ragsdale, S.W. Characterization of a three-component vanillate O-demethylase from Moorella thermoacetica. J. Bacteriol. 183 (2001) 3276-3281. [PMID: 11344134]
3. Pierce, E., Xie, G., Barabote, R.D., Saunders, E., Han, C.S., Detter, J.C., Richardson, P., Brettin, T.S., Das, A., Ljungdahl, L.G. and Ragsdale, S.W. The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ. Microbiol. 10 (2008) 2550-2573. [PMID: 18631365]
Accepted name: 6-deoxy-6-sulfo-D-fructose transketolase
Reaction: (1) 6-deoxy-6-sulfo-D-fructose + D-glyceraldehyde-3-phosphate = D-xylulose-5-phosphate + 4-deoxy-4-sulfo-D-erythrose
(2) 4-deoxy-4-sulfo-D-erythrulose + D-glyceraldehyde-3-phosphate = D-xylulose-5-phosphate + sulfoacetaldehyde
Other name(s): 6-deoxy-6-sulfo-erythrulose transketolase; sqwGH (gene name)
Systematic name: 6-deoxy-6-sulfo-D-fructose:D-glyceraldehyde-3-phosphate glycolaldehydetransferase
Comments: The enzyme, characterized from the bacterium Clostridium sp. MSTE9, is involved in a D-sulfoquinovose degradation pathway.
References:
1. Liu, J., Wei, Y., Ma, K., An, J., Liu, X., Liu, Y., Ang, E.L., Zhao, H. and Zhang, Y. Mechanistically diverse pathways for sulfoquinovose degradation in bacteria. ACS Catal. 11 (2021) 14740-14750.
Accepted name: tRNA-queuosine α-mannosyltransferase
Reaction: GDP-α-D-mannose + queuosine34 in tRNAAsp = GDP + O-4''-α-D-mannosylqueuosine34 in tRNAAsp
Other name(s): GDP-mannose:tRNAAsp-queuosine O-5''-β-D-mannosyltransferase (incorrect); tRNA-queuosine β-mannosyltransferase (incorrect)
Systematic name: GDP-α-D-mannose:queuosine34 in tRNAAsp O-4''-α-D-mannosyltransferase (configuration-retaining)
Comments: This enzyme, found in higher vertebrates, modifies tRNAAsp at the wobble position of the anticodon loop.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9055-06-5
References:
1. Okada, N. and Nishimura, S. Enzymatic synthesis of Q nucleoside containing mannose in the anticodon of tRNA: isolation of a novel mannosyltransferase from a cell-free extract of rat liver. Nucleic Acids Res. 4 (1977) 2931-2938. [PMID: 20603]
2. Hillmeier, M., Wagner, M., Ensfelder, T., Korytiakova, E., Thumbs, P., Muller, M. and Carell, T. Synthesis and structure elucidation of the human tRNA nucleoside mannosyl-queuosine. Nat. Commun. 12 (2021) 7123. [PMID: 34880214]
Accepted name: peptide-O-fucosyltransferase
Reaction: GDP-β-L-fucose + [protein]-(L-serine/L-threonine) = GDP + [protein]-3-O-(α-L-fucosyl)-(L-serine/L-threonine)
Other name(s): GDP-L-fucose:polypeptide fucosyltransferase; GDP-fucose protein O-fucosyltransferase; GDP-fucose:polypeptide fucosyltransferase; POFUT1 (gene name); POFUT2 (gene name)
Systematic name: GDP-β-L-fucose:protein-(L-serine/L-threonine) O-α-L-fucosyltransferase (configuration-inverting)
Comments: The enzyme, found in animals and plants, is involved in the biosynthesis of O-fucosylated proteins. In EGF domains, the attachment of O-linked fucose to serine or threonine occurs within the sequence Cys-Xaa-Xaa-Gly-Gly-Ser/Thr-Cys.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9033-08-3
References:
1. Wang, Y. and Spellman, M.W. Purification and characterization of a GDP-fucose:polypeptide fucosyltransferase from Chinese hamster ovary cells. J. Biol. Chem. 273 (1998) 8112-8118. [PMID: 9525914]
2. Wang, Y., Shao, L., Shi, S., Harris, R.J., Spellman, M.W., Stanley, P. and Haltiwanger, R.S. Modification of epidermal growth factor-like repeats with O-fucose. Molecular cloning and expression of a novel GDP-fucose protein O-fucosyltransferase. J. Biol. Chem. 276 (2001) 40338-40345. [PMID: 11524432]
3. Wang, Y., Lee, G.F., Kelley, R.F. and Spellman, M.W. Identification of a GDP-L-fucose:polypeptide fucosyltransferase and enzymatic addition of O-linked fucose to EGF domains. Glycobiology 6 (1996) 837-842. [PMID: 9023546]
4. Hofsteenge, J., Huwiler, K.G., Macek, B., Hess, D., Lawler, J., Mosher, D.F. and Peter-Katalinic, J. C-Mannosylation and O-fucosylation of the thrombospondin type 1 module. J. Biol. Chem. 276 (2001) 6485-6498. [PMID: 11067851]
5. Valero-Gonzalez, J., Leonhard-Melief, C., Lira-Navarrete, E., Jimenez-Oses, G., Hernandez-Ruiz, C., Pallares, M.C., Yruela, I., Vasudevan, D., Lostao, A., Corzana, F., Takeuchi, H., Haltiwanger, R.S. and Hurtado-Guerrero, R. A proactive role of water molecules in acceptor recognition by protein O-fucosyltransferase 2. Nat. Chem. Biol. 12 (2016) 240-246. [PMID: 26854667]
6. Zentella, R., Sui, N., Barnhill, B., Hsieh, W.P., Hu, J., Shabanowitz, J., Boyce, M., Olszewski, N.E., Zhou, P., Hunt, D.F. and Sun, T.P. The Arabidopsis O-fucosyltransferase SPINDLY activates nuclear growth repressor DELLA. Nat. Chem. Biol. 13 (2017) 479-485. [PMID: 28244988]
7. Lopaticki, S., Yang, A.SP., John, A., Scott, N.E., Lingford, J.P., O'Neill, M.T., Erickson, S.M., McKenzie, N.C., Jennison, C., Whitehead, L.W., Douglas, D.N., Kneteman, N.M., Goddard-Borger, E.D. and Boddey, J.A. Protein O-fucosylation in Plasmodium falciparum ensures efficient infection of mosquito and vertebrate hosts. Nat. Commun. 8 (2017) 561. [PMID: 28916755]
Accepted name: O-fucosylpeptide 3-β-N-acetylglucosaminyltransferase
Reaction: UDP-N-acetyl-α-D-glucosamine + [protein with EGF-like domain]-3-O-(α-L-fucosyl)-(L-serine/L-threonine) = UDP + [protein with EGF-like domain]-3-O-[N-acetyl-β-D-glucosaminyl-(1→3)-α-L-fucosyl]-(L-serine/L-threonine)
Glossary: EGF = epidermal growth factor
EGF-like domain = an evolutionary conserved domain containing 30 to 40 amino-acid residues first described from epidermal growth factor
Other name(s): O-fucosylpeptide β-1,3-N-acetylglucosaminyltransferase; fringe; UDP-D-GlcNAc:O-L-fucosylpeptide 3-β-N-acetyl-D-glucosaminyltransferase
Systematic name: UDP-N-acetyl-α-D-glucosamine:[protein with EGF-like domain]-3-O-(α-L-fucosyl)-(L-serine/L-threonine) 3-β-N-acetyl-D-glucosaminyltransferase (configuration-inverting)
Comments: The enzyme, found in animals and plants, is involved in the biosynthesis of the tetrasaccharides α-Neu5Ac-(2→3)-β-D-Gal-(1→4)-β-D-GlcNAc-(1→3)-α-L-Fuc and α-Neu5Ac-(2→6)-β-D-Gal-(1→4)-β-D-GlcNAc-(1→3)-α-L-Fuc, which are attached to L-Ser or L-Thr residues within the sequence Cys-Xaa-Xaa-Gly-Gly-Ser/Thr-Cys in EGF-like domains in Notch and Factor-X proteins, respectively. The substrate is provided by EC 2.4.1.221, peptide-O-fucosyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 299203-70-6
References:
1. Moloney, D.J., Panin, V.M., Johnston, S.H., Chen, J., Shao, L., Wilson, R., Wang, Y., Stanley, P., Irvine, K.D., Haltiwanger, R.S. and Vogt, T.F. Fringe is a glycosyltransferase that modifies Notch. Nature 406 (2000) 369-375. [PMID: 10935626]
2. Bruckner, K., Perez, L., Clausen, H. and Cohen, S. Glycosyltransferase activity of Fringe modulates Notch-Delta interactions. Nature 406 (2000) 411-415. [PMID: 10935637]
3. Rampal, R., Li, A.S., Moloney, D.J., Georgiou, S.A., Luther, K.B., Nita-Lazar, A. and Haltiwanger, R.S. Lunatic fringe, manic fringe, and radical fringe recognize similar specificity determinants in O-fucosylated epidermal growth factor-like repeats. J. Biol. Chem. 280 (2005) 42454-42463. [PMID: 16221665]
Accepted name: solabiose phosphorylase
Reaction: solabiose + phosphate = D-galactose + α-D-glucose 1-phosphate
Glossary: solabiose = β-D-glucopyranosyl-(1→3)-D-galactose
Systematic name: solabiose:phosphate α-D-glucosyltransferase
Comments: The enzyme, characterized from the bacterium Paenibacillus borealis, belongs to glycoside hydrolase family 94 (GH94).
References:
1. Saburi, W., Nihira, T., Nakai, H., Kitaoka, M. and Mori, H. Discovery of solabiose phosphorylase and its application for enzymatic synthesis of solabiose from sucrose and lactose. Sci. Rep. 12 (2022) 259. [PMID: 34997180]
Accepted name: lipopolysaccharide heptosyltransferase I
Reaction: ADP-L-glycero-β-D-manno-heptose + an α-Kdo-(2→4)-α-Kdo-(2→6)-[lipid A] = ADP + an α-Hep-(1→5)-[α-Kdo-(2→4)]-α-Kdo-(2→6)-[lipid A]
Glossary: Lipid A is a lipid component of the lipopolysaccharides (LPS) of Gram-negative bacteria. It consists of two glucosamine units connected by a β(1→6) bond and decorated with four to seven acyl chains and up to two phosphate groups.
Hep = L-glycero-D-manno-heptose
Other name(s): HepI; rfaC (gene name); WaaC; heptosyltransferase I (ambiguous)
Systematic name: ADP-L-glycero-β-D-manno-heptose:an α-Kdo-(2→4)-α-Kdo-(2→6)-[lipid A] 5-α-heptosyltransferase
Comments: The enzyme catalyses a glycosylation step in the biosynthesis of the inner core oligosaccharide of the lipopolysaccharide (endotoxin) of many Gram-negative bacteria.
References:
1. Kadrmas, J.L. and Raetz, C.R. Enzymatic synthesis of lipopolysaccharide in Escherichia coli. Purification and properties of heptosyltransferase i. J. Biol. Chem. 273 (1998) 2799-2807. [PMID: 9446588]
2. de Kievit, T.R. and Lam, J.S. Isolation and characterization of two genes, waaC (rfaC) and waaF (rfaF), involved in Pseudomonas aeruginosa serotype O5 inner-core biosynthesis. J. Bacteriol. 179 (1997) 3451-3457. [PMID: 9171387]
3. Klena, J.D., Gray, S.A. and Konkel, M.E. Cloning, sequencing, and characterization of the lipopolysaccharide biosynthetic enzyme heptosyltransferase I gene (waaC) from Campylobacter jejuni and Campylobacter coli. Gene 222 (1998) 177-185. [PMID: 9831648]
4. Gronow, S., Oertelt, C., Ervela, E., Zamyatina, A., Kosma, P., Skurnik, M. and Holst, O. Characterization of the physiological substrate for lipopolysaccharide heptosyltransferases I and II. J Endotoxin Res 7 (2001) 263-270. [PMID: 11717579]
5. Grizot, S., Salem, M., Vongsouthi, V., Durand, L., Moreau, F., Dohi, H., Vincent, S., Escaich, S. and Ducruix, A. Structure of the Escherichia coli heptosyltransferase WaaC: binary complexes with ADP and ADP-2-deoxy-2-fluoro heptose. J. Mol. Biol. 363 (2006) 383-394. [PMID: 16963083]
Accepted name: lipopolysaccharide heptosyltransferase II
Reaction: ADP-L-glycero-β-D-manno-heptose + an α-Hep-(1→5)-[α-Kdo-(2→4)]-α-Kdo-(2→6)-[lipid A] = ADP + an α-Hep-(1→3)-α-Hep-(1→5)-[α-Kdo-(2→4)]-α-Kdo-(2→6)-[lipid A]
Glossary: Lipid A is a lipid component of the lipopolysaccharides (LPS) of Gram-negative bacteria. It consists of two glucosamine units connected by a β(1→6) bond and decorated with four to seven acyl chains and up to two phosphate groups.
Hep = L-glycero-D-manno-heptose
Other name(s): HepII; rfaF (gene name); WaaF; heptosyltransferase II
Systematic name: ADP-L-glycero-β-D-manno-heptose:an α-L-glycero-D-manno-heptosyl-(1→5)-[α-Kdo-(2→4)]-α -Kdo-(2→6)-[lipid A] 3-α-heptosyltransferase
Comments: The enzyme catalyses a glycosylation step in the biosynthesis of the inner core oligosaccharide of the lipopolysaccharide (endotoxin) of some Gram-negative bacteria.
References:
1. Allen, A.G., Isobe, T. and Maskell, D.J. Identification and cloning of waaF (rfaF) from Bordetella pertussis and use to generate mutants of Bordetella spp. with deep rough lipopolysaccharide. J. Bacteriol. 180 (1998) 35-40. [PMID: 9422589]
2. Bauer, B.A., Lumbley, S.R. and Hansen, E.J. Characterization of a WaaF (RfaF) homolog expressed by Haemophilus ducreyi. Infect. Immun. 67 (1999) 899-907. [PMID: 9916106]
3. Gronow, S., Brabetz, W. and Brade, H. Comparative functional characterization in vitro of heptosyltransferase I (WaaC) and II (WaaF) from Escherichia coli. Eur. J. Biochem. 267 (2000) 6602-6611. [PMID: 11054112]
4. Gronow, S., Oertelt, C., Ervela, E., Zamyatina, A., Kosma, P., Skurnik, M. and Holst, O. Characterization of the physiological substrate for lipopolysaccharide heptosyltransferases I and II. J Endotoxin Res 7 (2001) 263-270. [PMID: 11717579]
5. Oldfield, N.J., Moran, A.P., Millar, L.A., Prendergast, M.M. and Ketley, J.M. Characterization of the Campylobacter jejuni heptosyltransferase II gene, waaF, provides genetic evidence that extracellular polysaccharide is lipid A core independent. J. Bacteriol. 184 (2002) 2100-2107. [PMID: 11914340]
Accepted name: lipopolysaccharide heptosyltransferase III
Reaction: ADP-L-glycero-β-D-manno-heptose + an α-Hep-(1→3)-4-O-phospho-α-Hep-(1→5)-[α-Kdo-(2→4)]-α-Kdo-(2→6)-[lipid A] = ADP + an α-Hep-(1→7)-α-Hep-(1→3)-4-O-phospho-α-Hep-(1→5)-[α-Kdo-(2→4)]-α-Kdo-(2→6)-[lipid A]
Glossary: Lipid A is a lipid component of the lipopolysaccharides (LPS) of Gram-negative bacteria. It consists of two glucosamine units connected by a β(1→6) bond and decorated with four to seven acyl chains and up to two phosphate groups.
Hep = L-glycero-D-manno-heptose
Other name(s): waaQ (gene name); rfaQ (gene name)
Systematic name: ADP-L-glycero-β-D-manno-heptose:an α-Hep-(1→3)-4-O-phospho-α-Hep-(1→5)-[α-Kdo-(2→4)]-α-Kdo-(2→6)-[lipid A] heptoseI 7-α-heptosyltransferase
Comments: The enzyme catalyses catalyses a glycosylation step in the biosynthesis of the inner core oligosaccharide of the lipopolysaccharide (endotoxin) of some Gram-negative bacteria.
References:
1. Mudapaka, J. and Taylor, E.A. Cloning and characterization of the Escherichia coli heptosyltransferase III: Exploring substrate specificity in lipopolysaccharide core biosynthesis. FEBS Lett. 589 (2015) 1423-1429. [PMID: 25957775]
Accepted name: phosphoglycerol geranylfarnesyltransferase
Reaction: all-trans-pentaprenyl diphosphate + sn-glycerol 1-phosphate = sn-3-O-(farnesylgeranyl)glycerol 1-phosphate + diphosphate
Other name(s): GFGP synthase
Systematic name: all-trans pentaprenyl diphosphate:sn-glycerol-1-phosphate pentaprenyltransferase
Comments: The enzyme, characterized from the archaeon Aeropyrum pernix, catalyses the first pathway-specific step in the biosynthesis of the core membrane C25,C25-diether lipids in some archaea. It does not act on geranylgeranyl diphosphate. cf. EC 2.5.1.41, phosphoglycerol geranylgeranyltransferase.
References:
1. Yoshida, R., Yoshimura, T. and Hemmi, H. Biosynthetic machinery for C25,C25-diether archaeal lipids from the hyperthermophilic archaeon Aeropyrum pernix. Biochem. Biophys. Res. Commun. 497 (2018) 87-92. [PMID: 29427665]
Accepted name: geranylfarnesylglycerol-phosphate geranylfarnesyltransferase
Reaction: all-trans-pentaprenyl diphosphate + sn-3-O-(farnesylgeranyl)glycerol 1-phosphate = 2,3-bis-O-(geranylfarnesyl)-sn-glycerol 1-phosphate + diphosphate
Other name(s): DGFGP synthase; 2,3-bis-O-(farnesylgeranyl)-sn-glycerol 1-phosphate synthase; 2,3-di-O-farnesylgeranylglyceryl synthase
Systematic name: all-trans-pentaprenyl diphosphate:sn-3-O-(pentaprenyl)glycerol 1-phosphate pentaprenyltransferase
Comments: The enzyme, characterized from the archaeon Aeropyrum pernix, carries out the second prenyltransfer reaction involved in the formation of C25,C25 membrane diether-lipids in some archaea. Requires a divalent metal cation, such as Mg2+. The enzyme cannot accept sn-3-(O-geranylgeranyl)glycerol 1-phosphate as the prenyl donor. cf. EC 2.5.1.42, geranylgeranylglycerol-phosphate geranylgeranyltransferase.
References:
1. Yoshida, R., Yoshimura, T. and Hemmi, H. Biosynthetic machinery for C25,C25-diether archaeal lipids from the hyperthermophilic archaeon Aeropyrum pernix. Biochem. Biophys. Res. Commun. 497 (2018) 87-92. [PMID: 29427665]
Accepted name: [amino-group carrier protein]-γ-(L-ornithyl)-L-glutamate aminotransferase
Reaction: an [amino-group carrier protein]-C-terminal-[γ-(L-ornithyl)-L-glutamate] + 2-oxoglutarate = an [amino-group carrier protein]-C-terminal-[γ-(L-glutamate 5-semialdehyde-2-yl)-L-glutamate] + L-glutamate
Other name(s): lysJ (gene name)
Systematic name: 2-oxoglutarate:[amino-group carrier protein]-C-terminal-[γ-(L-ornithyl)-L-glutamate] aminotransferase
Comments: The enzyme participates in an L-arginine biosynthetic pathway that operates in certain species of archaea. In some cases the enzyme also catalyses the activity of EC 2.6.1.118, [amino-group carrier protein]-γ-(L-lysyl)-L-glutamate aminotransferase.
References:
1. Yoshida, A., Tomita, T., Atomi, H., Kuzuyama, T. and Nishiyama, M. Lysine biosynthesis of Thermococcus kodakarensis with the capacity to function as an ornithine biosynthetic system. J. Biol. Chem. 291 (2016) 21630-21643. [PMID: 27566549]
Accepted name: GTP-dependent dephospho-CoA kinase
Reaction: GTP + 3'-dephospho-CoA = GDP + CoA
Systematic name: GTP:3'-dephospho-CoA 3'-phosphotransferase
Comments: The enzyme, characterized from the archaeon Thermococcus kodakarensis, participates in a coenzyme A biosynthesis pathway. cf. EC 2.7.1.24, dephospho-CoA kinase.
References:
1. Shimosaka, T., Makarova, K.S., Koonin, E.V. and Atomi, H. Identification of dephospho-coenzyme A (dephospho-CoA) kinase in Thermococcus kodakarensis and elucidation of the entire CoA biosynthesis pathway in archaea. mBio 10 (2019) . [PMID: 31337720]
Accepted name: phenol phosphorylase
Reaction: ATP + phenol + H2O = AMP + phenyl phosphate + phosphate
Other name(s): phenylphosphate synthase
Systematic name: ATP:phenol phosphotransferase (AMP-forming)
Comments: The enzyme, characterized from the bacterium Thauera aromatica, catalyses the first step in an anaerobic phenol degradation pathway. The enzyme, composed of three subunits, transfers the β-phosphoryl from ATP to phenol, forming phenyl phosphate, AMP, and phosphate [1]. During catalysis a diphosphoryl group is transferred from ATP to a histidine residue in one of the enzyme's subunits, from which phosphate is cleaved to render the reaction unidirectional. The remaining histidine phosphate subsequently serves as the actual phosphorylation agent [2].
References:
1. Schmeling, S., Narmandakh, A., Schmitt, O., Gad'on, N., Schuhle, K. and Fuchs, G. Phenylphosphate synthase: a new phosphotransferase catalyzing the first step in anaerobic phenol metabolism in Thauera aromatica. J. Bacteriol. 186 (2004) 8044-8057. [PMID: 15547277]
2. Narmandakh, A., Gad'on, N., Drepper, F., Knapp, B., Haehnel, W. and Fuchs, G. Phosphorylation of phenol by phenylphosphate synthase: role of histidine phosphate in catalysis. J. Bacteriol. 188 (2006) 7815-7822. [PMID: 16980461]
Accepted name: [amino-group carrier protein]-L-glutamate 6-kinase
Reaction: ATP + an [amino-group carrier protein]-C-terminal-γ-(L-glutamyl)-L-glutamate = ADP + an [amino-group carrier protein]-C-terminal-γ-(5-phospho-L-glutamyl)-L-glutamate
Other name(s): lysZ (gene name)
Systematic name: [amino-group carrier protein]-C-terminal-γ-(L-glutamyl)-L-glutamine 5-O-kinase
Comments: The enzyme participates in an L-arginine biosynthetic pathway in certain species of archaea. In some organisms the enzyme also catalyses the activity of EC 2.7.2.17, [amino-group carrier protein]-L-2-aminoadipate 6-kinase.
References:
1. Ouchi, T., Tomita, T., Horie, A., Yoshida, A., Takahashi, K., Nishida, H., Lassak, K., Taka, H., Mineki, R., Fujimura, T., Kosono, S., Nishiyama, C., Masui, R., Kuramitsu, S., Albers, S.V., Kuzuyama, T. and Nishiyama, M. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat. Chem. Biol. 9 (2013) 277-283. [PMID: 23434852]
2. Yoshida, A., Tomita, T., Atomi, H., Kuzuyama, T. and Nishiyama, M. Lysine biosynthesis of Thermococcus kodakarensis with the capacity to function as an ornithine biosynthetic system. J. Biol. Chem. 291 (2016) 21630-21643. [PMID: 27566549]
Accepted name: inositol-hexakisphosphate 5-kinase
Reaction: (1) ATP + 1D-myo-inositol hexakisphosphate = ADP + 1D-myo-inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate
(2) ATP + 1D-myo-inositol 1-diphosphate 2,3,4,5,6-pentakisphosphate = ADP + 1D-myo-inositol 1,5-bis(diphosphate) 2,3,4,6-tetrakisphosphate
Other name(s): ATP:1D-myo-inositol-hexakisphosphate phosphotransferase; IP6K; inositol-hexakisphosphate kinase (ambiguous)
Systematic name: ATP:1D-myo-inositol-hexakisphosphate 5-phosphotransferase
Comments: Three mammalian isoforms are known to exist.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 176898-37-6
References:
1. Saiardi, A., Erdjument-Bromage, H., Snowman, A.M., Tempst, P. and Snyder, S.H. Synthesis of diphosphoinositol pentakisphosphate by a newly identified family of higher inositol polyphosphate kinases. Curr. Biol. 9 (1999) 1323-1326. [PMID: 10574768]
2. Schell, M.J., Letcher, A.J., Brearley, C.A., Biber, J., Murer, H. and Irvine, R.F. PiUS (Pi uptake stimulator) is an inositol hexakisphosphate kinase. FEBS Lett. 461 (1999) 169-172. [PMID: 10567691]
3. Albert, C., Safrany, S.T., Bembenek, M.E., Reddy, K.M., Reddy, K.K., Falck, J.-R., Bröcker, M., Shears, S.B. and Mayr, G.W. Biological variability in the structures of diphosphoinositol polyphosphates in Dictyostelium discoideum and mammalian cells. Biochem. J. 327 (1997) 553-560. [PMID: 9359429]
4. Lin, H., Fridy, P.C., Ribeiro, A.A., Choi, J.H., Barma, D.K., Vogel, G., Falck, J.R., Shears, S.B., York, J.D. and Mayr, G.W. Structural analysis and detection of biological inositol pyrophosphates reveal that the family of VIP/diphosphoinositol pentakisphosphate kinases are 1/3-kinases. J. Biol. Chem. 284 (2009) 1863-1872. [PMID: 18981179]
5. Wang, H., Falck, J.R., Hall, T.M. and Shears, S.B. Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding. Nat. Chem. Biol. 8 (2012) 111-116. [PMID: 22119861]
Accepted name: diphosphoinositol-pentakisphosphate 1-kinase
Reaction: (1) ATP + 1D-myo-inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate = ADP + 1D-myo-inositol 1,5-bis(diphosphate) 2,3,4,6-tetrakisphosphate
(2) ATP + 1D-myo-inositol hexakisphosphate = ADP + 1D-myo-inositol 1-diphosphate 2,3,4,5,6-pentakisphosphate
Other name(s): PP-IP5 kinase; diphosphoinositol pentakisphosphate kinase; ATP:5-diphospho-1D-myo-inositol-pentakisphosphate phosphotransferase; PP-InsP5 kinase; PPIP5K; PPIP5K1; PPIP5K2; VIP1; VIP2; diphosphoinositol-pentakisphosphate 1/3-kinase (incorrect); diphosphoinositol-pentakisphosphate kinase (ambiguous)
Systematic name: ATP:1D-myo-inositol-5-diphosphate-pentakisphosphate 1-phosphotransferase
Comments: This enzyme is activated by osmotic shock [4]. Ins(1,3,4,5,6)P5, 1D-myo-inositol diphosphate tetrakisphosphate and 1D-myo-inositol bisdiphosphate triphosphate are not substrates [4]. The enzyme specifically phosphorylates the 1-position of the substrates [6].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Shears, S.B., Ali, N., Craxton, A. and Bembenek, M.E. Synthesis and metabolism of bis-diphosphoinositol tetrakisphosphate in vitro and in vivo. J. Biol. Chem. 270 (1995) 10489-10497. [PMID: 7737983]
2. Albert, C., Safrany, S.T., Bembenek, M.E., Reddy, K.M., Reddy, K.K., Falck, J.-R., Bröcker, M., Shears, S.B. and Mayr, G.W. Biological variability in the structures of diphosphoinositol polyphosphates in Dictyostelium discoideum and mammalian cells. Biochem. J. 327 (1997) 553-560. [PMID: 9359429]
3. Fridy, P.C., Otto, J.C., Dollins, D.E. and York, J.D. Cloning and characterization of two human VIP1-like inositol hexakisphosphate and diphosphoinositol pentakisphosphate kinases. J. Biol. Chem. 282 (2007) 30754-30762. [PMID: 17690096]
4. Choi, J.H., Williams, J., Cho, J., Falck, J.R. and Shears, S.B. Purification, sequencing, and molecular identification of a mammalian PP-InsP5 kinase that Is activated when cells are exposed to hyperosmotic stress. J. Biol. Chem. 282 (2007) 30763-30775. [PMID: 17702752]
5. Lin, H., Fridy, P.C., Ribeiro, A.A., Choi, J.H., Barma, D.K., Vogel, G., Falck, J.R., Shears, S.B., York, J.D. and Mayr, G.W. Structural analysis and detection of biological inositol pyrophosphates reveal that the family of VIP/diphosphoinositol pentakisphosphate kinases are 1/3-kinases. J. Biol. Chem. 284 (2009) 1863-1872. [PMID: 18981179]
6. Wang, H., Falck, J.R., Hall, T.M. and Shears, S.B. Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding. Nat. Chem. Biol. 8 (2012) 111-116. [PMID: 22119861]
Accepted name: cAMP-dependent protein kinase
Reaction: ATP + a [protein]-(L-serine/L-threonine) = ADP + a [protein]-(L-serine/L-threonine) phosphate
Glossary: 3',5'-cyclic-AMP = cAMP
Other name(s): PKA; protein kinase A; PKA catalytic (C) subunit; A kinase; ATP:protein phosphotransferase (cAMP-dependent)
Systematic name: ATP:protein Ser/Thr-phosphotransferase (3',5'-cAMP-dependent)
Comments: This eukaryotic enzyme recognizes the sequence -Arg-Arg-X-Ser*/Thr*-Hpo, where * indicates the phosphorylated residue and Hpo indicates a hydrophobic residue.The inactive holoenzyme is a heterotetramer composed of two regulatory (R) subunits and two catalytic (C) subunits. Each R subunit occludes the active site of a C subunit and contains two binding sites for 3',5'-cyclic-AMP (cAMP). Binding of cAMP activates the enzyme by causing conformational changes that release two free monomeric C subunits from a dimer of the R subunits, i.e. R2C2 + 4 cAMP = R2(cAMP)4 + 2 C. Activity requires phosphorylation of a conserved Thr in the activation loop (T-loop) sequence (Thr198 in human Cα; Thr224 in budding yeast Tpk2), installed by auto-phosphorylation or by the 3-phosphoinositide-dependent protein kinase-1 (PDPK1). Certain R2C2 combinations can be localized to particular subcellular regions by their association with diverse species of 'A Kinase-Anchoring Proteins' (AKAPs). The enzyme has been characterized from many organisms. Humans have three C units (Cα, Cβ, and Cγ) encoded by the paralogous genes PRKACA, PRKACB and PRKACG, respectively, and four R subunits (R1α, RIβ, RIIα and RIIβ), encoded by PKRAR1A, PKRAR1B, PKRAR2A and PKRAR2B, respectively. Yeast (Saccharomyces cerevisiae) has three C subunits (Tpk1, Tpk2, and Tpk3) encoded by the paralogous genes TPK1, TPK2 and TPK3, respectively, and a single R subunit (Bcy1) encoded by the BCY1 gene. Some validated substrates of the enzyme include cAMP-response element-binding protein (CREB), phosphorylase kinase α subunit (PHKA), and tyrosine 3-monooxygenase (TH) in mammals; Adr1, Whi3, Nej1, and Pyk1 in yeast.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 142008-29-5
References:
1. Krebs, E.G. The Albert Lasker Medical Awards. Role of the cyclic AMP-dependent protein kinase in signal transduction. JAMA 262 (1989) 1815-1818. [PMID: 2550680]
2. Technikova-Dobrova, Z., Sardanelli, A.M., Speranza, F., Scacco, S., Signorile, A., Lorusso, V. and Papa, S. Cyclic adenosine monophosphate-dependent phosphorylation of mammalian mitochondrial proteins: enzyme and substrate characterization and functional role. Biochemistry 40 (2001) 13941-13947. [PMID: 11705384]
3. Smith, F.D., Samelson, B.K. and Scott, J.D. Discovery of cellular substrates for protein kinase A using a peptide array screening protocol. Biochem. J. 438 (2011) 103-110. [PMID: 21644927]
4. Broach, J.R. Nutritional control of growth and development in yeast. Genetics 192 (2012) 73-105. [PMID: 22964838]
5. Embogama, D.M. and Pflum, M.K. K-BILDS: A kinase substrate discovery tool. Chembiochem 18 (2017) 136-141. [PMID: 27860220]
6. Taylor, S.S., Wu, J., Bruystens, J.GH., Del Rio, J.C., Lu, T.W., Kornev, A.P. and Ten Eyck, L.F. From structure to the dynamic regulation of a molecular switch: A journey over 3 decades. J. Biol. Chem. 296 (2021) 100746. [PMID: 33957122]
7. Ramms, D.J., Raimondi, F., Arang, N., Herberg, F.W., Taylor, S.S. and Gutkind, J.S. Galphas-protein kinase A (PKA) pathway signalopathies: The emerging genetic landscape and therapeutic potential of human diseases driven by aberrant Galphas-PKA signaling. Pharmacol Rev 73 (2021) 155-197. [PMID: 34663687]
Accepted name: NEK6-subfamily protein kinase
Reaction: ATP + a [protein]-(L-serine/L-threonine) = ADP + a [protein]-(L-serine/L-threonine) phosphate
Other name(s): NEK6; NEK7; nekl-3
Comments: Requires Mg2+. NEK6 subfamily kinases are present in animals, though lost in insects, and include human NEK6 and NEK7 and C. elegans nekl-3. They are activated in mitosis by phosphorylation by NEK9 [1], and phosphorylate cytoskeletal proteins including EML4, KIF11A and KIF14 [4,2]. In C. elegans, nekl-3 is involved in clathrin-mediated endocytosis [5]. In peptide arrays, NEK6 prefers to phosphorylate Ser residues, with hydrophobic residues at -2 and +1 and charged residues at -1, -2 and +2 [3].
References:
1. Belham, C., Roig, J., Caldwell, J.A., Aoyama, Y., Kemp, B.E., Comb, M. and Avruch, J. A mitotic cascade of NIMA family kinases. Nercc1/Nek9 activates the Nek6 and Nek7 kinases. J. Biol. Chem. 278 (2003) 34897-34909. [PMID: 12840024]
2. Cullati, S.N., Kabeche, L., Kettenbach, A.N. and Gerber, S.A. A bifurcated signaling cascade of NIMA-related kinases controls distinct kinesins in anaphase. J. Cell Biol. 216 (2017) 2339-2354. [PMID: 28630147]
3. van de Kooij, B., Creixell, P., van Vlimmeren, A., Joughin, B.A., Miller, C.J., Haider, N., Simpson, C.D., Linding, R., Stambolic, V., Turk, B.E. and Yaffe, M.B. Comprehensive substrate specificity profiling of the human Nek kinome reveals unexpected signaling outputs. Elife 8 (2019) . [PMID: 31124786]
4. Adib, R., Montgomery, J.M., Atherton, J., O'Regan, L., Richards, M.W., Straatman, K.R., Roth, D., Straube, A., Bayliss, R., Moores, C.A. and Fry, A.M. Mitotic phosphorylation by NEK6 and NEK7 reduces the microtubule affinity of EML4 to promote chromosome congression. Sci Signal 12 (2019) . [PMID: 31409757]
5. Joseph, B.B., Wang, Y., Edeen, P., Lazetic, V., Grant, B.D. and Fay, D.S. Control of clathrin-mediated endocytosis by NIMA family kinases. PLoS Genet. 16 (2020) e1008633. [PMID: 32069276]
[EC 3.3.1.1 Transferred entry: adenosylhomocysteinase, now classified as EC 3.13.2.1, adenosylhomocysteinase (EC 3.3.1.1 created 1961, modified 2004, deleted 2022)]
[EC 3.3.1.2 Transferred entry: S-adenosyl-L-methionine hydrolase (L-homoserine-forming), now classified as EC 3.13.2.2, S-adenosyl-L-methionine hydrolase (L-homoserine-forming) (EC 3.3.1.2 created 1972, modified 1976, modified 2018, deleted 2022)]
Accepted name: matriptase
Reaction: Cleaves various synthetic substrates with Arg or Lys at the P1 position and prefers small side-chain amino acids, such as Ala and Gly, at the P2 position
Other name(s): serine protease 14; membrane-type serine protease 1; MT-SP1; prostamin; serine protease TADG-15; tumor-associated differentially-expressed gene 15 protein; ST14; breast cancer 80 kDa protease; epithin; serine endopeptidase SNC19; matriptase-1; matriptase-2; matriptase-3; TMPRSS6 (gene name)
Comments: This trypsin-like integral-membrane serine peptidase has been implicated in breast cancer invasion and metastasis [1,2]. The enzyme can activate hepatocyte growth factor/scattering factor (HGF/SF) by cleavage of the two-chain form at an Arg residue to give active α- and β-HGF, but It does not activate plasminogen, which shares high homology with HGF [1]. The enzyme can also activate urokinase plasminogen activator (uPA), which initiates the matrix-degrading peptidase cascade [1,2]. Hemojuvelin has been shown to be a physiologic substrate for matriptase-2 [5]. Belongs in peptidase family S1A.
Links to other databases: BRENDA, EXPASY, KEGG, MEROPS, MetaCyc, PDB, CAS registry number: 241475-96-7
References:
1. Lee, S.L., Dickson, R.B. and Lin, C.Y. Activation of hepatocyte growth factor and urokinase/plasminogen activator by matriptase, an epithelial membrane serine protease. J. Biol. Chem. 275 (2000) 36720-36725. [PMID: 10962009]
2. Lin, C.Y., Anders, J., Johnson, M., Sang, Q.A. and Dickson, R.B. Molecular cloning of cDNA for matriptase, a matrix-degrading serine protease with trypsin-like activity. J. Biol. Chem. 274 (1999) 18231-18236. [PMID: 10373424]
3. Ramsay, A.J., Reid, J.C., Velasco, G., Quigley, J.P. and Hooper, J.D. The type II transmembrane serine protease matriptase-2 – identification, structural features, enzymology, expression pattern and potential roles. Front. Biosci. 13 (2008) 569-579. [PMID: 17981570]
4. Kojima, K., Tsuzuki, S., Fushiki, T. and Inouye, K. The activity of a type II transmembrane serine protease, matriptase, is dependent solely on the catalytic domain. Biosci. Biotechnol. Biochem. 73 (2009) 454-456. [PMID: 19202271]
5. Wysocka, M., Gruba, N., Miecznikowska, A., Popow-Stellmaszyk, J., Gutschow, M., Stirnberg, M., Furtmann, N., Bajorath, J., Lesner, A. and Rolka, K. Substrate specificity of human matriptase-2. Biochimie 97 (2014) 121-127. [PMID: 24161741]
Accepted name: transmembrane protease serine 2
Reaction: The enzyme cleaves angiotensin-converting enzyme 2 (EC 3.4.17.23) and cleaves influenzea A and B virus and coronavirus spike glycoproteins at arginine residues.
Other name(s): TMPRSS2 (gene name); epitheliasin
Comments: The enzyme, present in mammalia, cleaves and inactivates EC 3.4.17.23, angiotensin-converting enzyme 2 (ACE2) at arginine residues in the region R697 to R716, which enhances influenza and coronavirus uptake [7] The enzyme also cleaves and activates influenza and coronavirus spike glycoproteins and thus facilitates virus-cell membrane fusions. The cleavage of SARS-COV2 spike glycoprotein occurs between the S2 and S2' site at SKPSKR/SFIEDL, while the cleavage of MERS-COV glycoprotein occurs at GSRSAR/SAIEDL
References:
1. Jacquinet, E., Rao, N.V., Rao, G.V. and Hoidal, J.R. Cloning, genomic organization, chromosomal assignment and expression of a novel mosaic serine proteinase: epitheliasin. FEBS Lett. 468 (2000) 93-100. [PMID: 10683448]
2. Jacquinet, E., Rao, N.V., Rao, G.V., Zhengming, W., Albertine, K.H. and Hoidal, J.R. Cloning and characterization of the cDNA and gene for human epitheliasin. Eur. J. Biochem. 268 (2001) 2687-2699. [PMID: 11322890]
3. Bottcher-Friebertshauser, E., Freuer, C., Sielaff, F., Schmidt, S., Eickmann, M., Uhlendorff, J., Steinmetzer, T., Klenk, H.D. and Garten, W. Cleavage of influenza virus hemagglutinin by airway proteases TMPRSS2 and HAT differs in subcellular localization and susceptibility to protease inhibitors. J. Virol. 84 (2010) 5605-5614. [PMID: 20237084]
4. Bertram, S., Glowacka, I., Muller, M.A., Lavender, H., Gnirss, K., Nehlmeier, I., Niemeyer, D., He, Y., Simmons, G., Drosten, C., Soilleux, E.J., Jahn, O., Steffen, I. and Pohlmann, S. Cleavage and activation of the severe acute respiratory syndrome coronavirus spike protein by human airway trypsin-like protease. J. Virol. 85 (2011) 13363-13372. [PMID: 21994442]
5. Bertram, S., Dijkman, R., Habjan, M., Heurich, A., Gierer, S., Glowacka, I., Welsch, K., Winkler, M., Schneider, H., Hofmann-Winkler, H., Thiel, V. and Pohlmann, S. TMPRSS2 activates the human coronavirus 229E for cathepsin-independent host cell entry and is expressed in viral target cells in the respiratory epithelium. J. Virol. 87 (2013) 6150-6160. [PMID: 23536651]
6. Abe, M., Tahara, M., Sakai, K., Yamaguchi, H., Kanou, K., Shirato, K., Kawase, M., Noda, M., Kimura, H., Matsuyama, S., Fukuhara, H., Mizuta, K., Maenaka, K., Ami, Y., Esumi, M., Kato, A. and Takeda, M. TMPRSS2 is an activating protease for respiratory parainfluenza viruses. J. Virol. 87 (2013) 11930-11935. [PMID: 23966399]
7. Heurich, A., Hofmann-Winkler, H., Gierer, S., Liepold, T., Jahn, O. and Pohlmann, S. TMPRSS2 and ADAM17 cleave ACE2 differentially and only proteolysis by TMPRSS2 augments entry driven by the severe acute respiratory syndrome coronavirus spike protein. J. Virol. 88 (2014) 1293-1307. [PMID: 24227843]
8. Limburg, H., Harbig, A., Bestle, D., Stein, D.A., Moulton, H.M., Jaeger, J., Janga, H., Hardes, K., Koepke, J., Schulte, L., Koczulla, A.R., Schmeck, B., Klenk, H.D. and Bottcher-Friebertshauser, E. TMPRSS2 is the major activating protease of influenza A virus in primary human airway cells and influenza B virus in human type II pneumocytes. J. Virol. 93 (2019) . [PMID: 31391268]
9. Bestle, D., Heindl, M.R., Limburg, H., Van Lam van, T., Pilgram, O., Moulton, H., Stein, D.A., Hardes, K., Eickmann, M., Dolnik, O., Rohde, C., Klenk, H.D., Garten, W., Steinmetzer, T. and Bottcher-Friebertshauser, E. TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells. Life Sci Alliance 3 (2020) . [PMID: 32703818]
[EC 3.13.1.8 Transferred entry: S-adenosyl-L-methionine hydrolase (adenosine-forming), now classified as EC 3.13.2.3, S-adenosyl-L-methionine hydrolase (adenosine-forming) (EC 3.13.1.8 created 2018, deleted 2022)]
EC 3.13 Acting on carbon-sulfur bonds
EC 3.13.2 Thioether and trialkylsulfonium hydrolases
Accepted name: adenosylhomocysteinase
Reaction: S-adenosyl-L-homocysteine + H2O = L-homocysteine + adenosine
For diagram of reaction mechanism, click here
Other name(s): S-adenosylhomocysteine synthase; S-adenosylhomocysteine hydrolase (ambiguous); adenosylhomocysteine hydrolase; S-adenosylhomocysteinase; SAHase; AdoHcyase
Systematic name: S-adenosyl-L-homocysteine hydrolase
Comments: The enzyme contains one tightly bound NAD+ per subunit. This appears to bring about a transient oxidation at C-3' of the 5'-deoxyadenosine residue, thus labilizing the thioether bond [2] (for mechanism, click here), cf. EC 5.5.1.4, inositol-3-phosphate synthase.
References:
1. de la Haba, G. and Cantoni, G.L. The enzymatic synthesis of S-adenosyl-L-homocysteine from adenosine and homocysteine. J. Biol. Chem. 234 (1959) 603-608. [PMID: 13641268]
2. Palmer, J.L. and Abeles, R.H. The mechanism of action of S-adenosylhomocysteinase. J. Biol. Chem. 254 (1979) 1217-1226. [PMID: 762125]
Accepted name: S-adenosyl-L-methionine hydrolase (L-homoserine-forming)
Reaction: S-adenosyl-L-methionine + H2O = L-homoserine + S-methyl-5'-thioadenosine
Glossary: S-methyl-L-methionine sulfonium salt = (S)-3-amino-3-carboxypropyldi(methyl)sulfonium salt
Other name(s): S-adenosylmethionine cleaving enzyme; methylmethionine-sulfonium-salt hydrolase; adenosylmethionine lyase; adenosylmethionine hydrolase; S-adenosylmethionine hydrolase; S-adenosyl-L-methionine hydrolase
Systematic name: S-adenosyl-L-methionine hydrolase (L-homoserine-forming)
Comments: Also hydrolyses S-methyl-L-methionine to dimethyl sulfide and homoserine. cf. EC 3.13.2.3, (R)-S-adenosyl-L-methionine hydrolase (adenosine-forming).
References:
1. Mazelis, M., Levin, B. and Mallinson, N. Decomposition of methyl methionine sulfonium salts by a bacterial enzyme. Biochim. Biophys. Acta 105 (1965) 106-114. [PMID: 5849106]
Accepted name: (R)-S-adenosyl-L-methionine hydrolase (adenosine-forming)
Reaction: (R)-S-adenosyl-L-methionine + H2O = adenosine + L-methionine
Other name(s): SAM hydroxide adenosyltransferase
Systematic name: (R)-S-adenosyl-L-methionine hydrolase (adenosine-forming)
Comments: The enzyme, found in bacteria and archaea, is involved in removing the (R) isomer of S-adenosyl-L-methionine from the cell. It catalyses a nucleophilic attack of water at the C5' carbon of S-adenosyl-L-methionine to generate adenosine and L-methionine.
References:
1. Eustaquio, A.S., Harle, J., Noel, J.P. and Moore, B.S. S-Adenosyl-L-methionine hydrolase (adenosine-forming), a conserved bacterial and archaeal protein related to SAM-dependent halogenases. ChemBioChem 9 (2008) 2215-2219. [PMID: 18720493]
2. Deng, H., McMahon, S.A., Eustaquio, A.S., Moore, B.S., Naismith, J.H. and O'Hagan, D. Mechanistic insights into water activation in SAM hydroxide adenosyltransferase (duf-62). ChemBioChem 10 (2009) 2455-2459. [PMID: 19739191]
3. Kornfuehrer, T., Romanowski, S., de Crecy-Lagard, V., Hanson, A.D. and Eustaquio, A.S. An enzyme containing the conserved domain of unknown function DUF62 acts as a stereoselective (Rs ,Sc)-S-adenosylmethionine hydrolase. Chembiochem 21 (2020) 3495-3499. [PMID: 32776704]
Accepted name: L-cysteate decarboxylase
Reaction: L-cysteate = taurine + CO2
Other name(s): CAD
Systematic name: L-cysteate carboxy-lyase (taurine-forming)
Comments: Requires pyridoxal 5'-phosphate. The enzyme, characterized from chicken, is specific for L-cysteate and has poor activity with 3-sulfino-L-alanine. cf. EC 4.1.1.29, sulfinoalanine decarboxylase.
References:
1. Malatesta, M., Mori, G., Acquotti, D., Campanini, B., Peracchi, A., Antin, P.B. and Percudani, R. Birth of a pathway for sulfur metabolism in early amniote evolution. Nat Ecol Evol 4 (2020) 1239-1246. [PMID: 32601391]
Accepted name: phenyl-phosphate phosphatase/carboxylase
Reaction: 4-hydroxybenzoate + phosphate = phenyl phosphate + CO2 + H2O
Other name(s): phenyl phosphate carboxylase
Systematic name: 4-hydroxybenzoate carboxy-lyase (phenyl phosphate-forming)
Comments: The enzyme, characterized from the bacterium Thauera aromatica, participates in an anaerobic phenol degradation pathway. It catalyses the para dephosphorylation and carboxylation of phenylphosphate to 4-hydroxybenzoate. The enzyme from Thauera aromatica consists of four different subunits and requires K+ and a divalent metal cation (Mg2+ or Mn2+) for activity. It is strongly inhibited by oxygen.
References:
1. Schuhle, K. and Fuchs, G. Phenylphosphate carboxylase: a new C-C lyase involved in anaerobic phenol metabolism in Thauera aromatica. J. Bacteriol. 186 (2004) 4556-4567. [PMID: 15231788]
Accepted name: medium-chain-enoyl-CoA hydratase
Reaction: a medium-chain (3S)-3-hydroxyacyl-CoA = a medium-chain trans-2-enoyl-CoA + H2O
Glossary: a medium-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 6 to 12 carbon atoms.
Other name(s): long-chain enoyl coenzyme A hydratase (incorrect); long-chain-enoyl-CoA hydratase (incorrect); long-chain-(3S)-3-hydroxyacyl-CoA hydro-lyase (incorrect)
Systematic name: medium-chain-(3S)-3-hydroxyacyl-CoA hydro-lyase
Comments: Acts in the reverse direction. The best substrate for the porcine enzyme is oct-2-enoyl-CoA. Unlike EC 4.2.1.17 enoyl-CoA hydratase, it does not act on crotonoyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 62009-81-8
References:
1. Fong, J.C. and Schulz, H. Purification and properties of pig heart crotonase and the presence of short chain and long chain enoyl coenzyme A hydratases in pig and guinea pig tissues. J. Biol. Chem. 252 (1977) 542-547. [PMID: 833142]
2. Schulz, H. Long chain enoyl coenzyme A hydratase from pig heart. J. Biol. Chem. 249 (1974) 2704-2709. [PMID: 4828315]
3. Arent, S., Christensen, C.E., Pye, V.E., Norgaard, A. and Henriksen, A. The multifunctional protein in peroxisomal β-oxidation: structure and substrate specificity of the Arabidopsis thaliana protein MFP2. J. Biol. Chem. 285 (2010) 24066-24077. [PMID: 20463021]
Accepted name: uridylate cyclase
Reaction: UTP = 3',5'-cyclic UMP + diphosphate
Glossary: 3',5'-cyclic UMP = cUMP
uridylate = CMP
Other name(s): pycC (gene name) (ambiguous)
Systematic name: UTP diphosphate-lyase (cyclizing; 3',5'-cyclic-UMP-forming)
Comments: The enzyme, found in bacteria and archaea, forms cUMP, which functions as a second messenger in bacterial immunity against viruses. The enzyme is synthesized following phage infection and activates immune effectors that execute an antiviral response.
References:
1. Tal, N., Morehouse, B.R., Millman, A., Stokar-Avihail, A., Avraham, C., Fedorenko, T., Yirmiya, E., Herbst, E., Brandis, A., Mehlman, T., Oppenheimer-Shaanan, Y., Keszei, A.FA., Shao, S., Amitai, G., Kranzusch, P.J. and Sorek, R. Cyclic CMP and cyclic UMP mediate bacterial immunity against phages. Cell 184 (2021) 5728-5739.e16. [PMID: 34644530]
Accepted name: sulfoquinovose isomerase
Reaction: (1) β-sulfoquinovose = 6-deoxy-6-sulfo-D-fructose
(2) β-sulfoquinovose = 6-sulfo-D-rhamnose
For diagram of reaction, click here
Glossary: sulfoquinovose = 6-deoxy-6-sulfo-D-glucopyranose
Other name(s): yihS (gene name)
Systematic name: 6-deoxy-6-sulfo-β-D-glucopyranose aldose-ketose-isomerase
Comments: The enzyme, characterized from the bacterium Escherichia coli, is involved in the degradation pathway of sulfoquinovose, the polar headgroup of sulfolipids found in the photosynthetic membranes of all higher plants, mosses, ferns, algae, and most photosynthetic bacteria, as well as the surface layer of some archaea.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Denger, K., Weiss, M., Felux, A.K., Schneider, A., Mayer, C., Spiteller, D., Huhn, T., Cook, A.M. and Schleheck, D. Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle. Nature 507 (2014) 114-117. [PMID: 24463506]
2. Sharma, M., Abayakoon, P., Epa, R., Jin, Y., Lingford, J.P., Shimada, T., Nakano, M., Mui, J.W., Ishihama, A., Goddard-Borger, E.D., Davies, G.J. and Williams, S.J. Molecular basis of sulfosugar selectivity in sulfoglycolysis. ACS Cent. Sci. 7 (2021) 476-487. [PMID: 33791429]
Accepted name: 4-deoxy-4-sulfo-D-erythrose isomerase
Reaction: 4-deoxy-4-sulfo-D-erythrose = 4-deoxy-4-sulfo-D-erythrulose
Other name(s): sqwI (gene name)
Systematic name: 4-deoxy-4-sulfo-D-erythrose ketose-aldose isomerase
Comments: The enzyme, characterized from the bacterium Clostridium sp. MSTE9, is involved in a D-sulfoquinovose degradation pathway.
References:
1. Liu, J., Wei, Y., Ma, K., An, J., Liu, X., Liu, Y., Ang, E.L., Zhao, H. and Zhang, Y. Mechanistically diverse pathways for sulfoquinovose degradation in bacteria. ACS Catal. 11 (2021) 14740-14750.
Accepted name: succinate dehydrogenase (electrogenic, proton-motive force generating)
Reaction: succinate + menaquinone + 2 H+[side 1] = fumarate + menaquinol + 2 H+[side 2]
Systematic name: succinate:quinone oxidoreductase (electrogenic, proton-motive force generating)
Comments: The enzyme is very similar to EC 1.3.5.1, succinate dehydrogenase, but differs by containing two heme molecules (located in the membrane anchor component) in addition to FAD and three iron-sulfur clusters. Unlike EC 1.3.5.1, this enzyme catalyses an electrogenic reaction, enabled by electron-bifurcation via the heme molecules. In the direction of succinate oxidation by menaquinone, which is endergonic, the reaction is driven by the transmembrane electrochemical proton potential. In the direction of fumarate reduction, the electrogenic electron transfer reaction is compensated by transmembrane proton transfer pathway known as the E-pathway, which results in overall electroneutrality.
References:
1. Lancaster, C.R. Wolinella succinogenes quinol:fumarate reductase-2.2-A resolution crystal structure and the E-pathway hypothesis of coupled transmembrane proton and electron transfer. Biochim. Biophys. Acta 1565 (2002) 215-231. [PMID: 12409197]
2. Madej, M.G., Nasiri, H.R., Hilgendorff, N.S., Schwalbe, H., Unden, G. and Lancaster, C.R. Experimental evidence for proton motive force-dependent catalysis by the diheme-containing succinate:menaquinone oxidoreductase from the Gram-positive bacterium Bacillus licheniformis. Biochemistry 45 (2006) 15049-15055. [PMID: 17154542]
3. Lancaster, C.R., Herzog, E., Juhnke, H.D., Madej, M.G., Muller, F.G., Paul, R. and Schleidt, P.G. Electroneutral and electrogenic catalysis by dihaem-containing succinate:quinone oxidoreductases. Biochem Soc Trans. 36 (2008) 996-1000. [PMID: 18793177]
4. Lancaster, C.R. The di-heme family of respiratory complex II enzymes. Biochim. Biophys. Acta 1827 (2013) 679-687. [PMID: 23466335]
5. Guan, H.H., Hsieh, Y.C., Lin, P.J., Huang, Y.C., Yoshimura, M., Chen, L.Y., Chen, S.K., Chuankhayan, P., Lin, C.C., Chen, N.C., Nakagawa, A., Chan, S.I. and Chen, C.J. Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas. Sci. Rep. 8 (2018) 14935. [PMID: 30297797]