An asterisk before "EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: cyclohexane-1-carbonyl-CoA reductase (NADP+)
Reaction: cyclohexane-1-carbonyl-CoA + NADP+ = cyclohex-1-ene-1-carbonyl-CoA + NADPH + H+
Other name(s): 1-cyclohexenylcarbonyl-CoA reductase (ambiguous); chcA (gene name)
Systematic name: cyclohexane-1-carbonyl-CoA:NADP+ 1-oxidoreductase
Comments: The enzyme, characterized from the bacterium Streptomyces collinus, is involved in a pathway that transforms shikimate to cyclohexane-1-carbonyl-CoA by a series of dehydration and double-bond reduction steps. Most of the steps in this process occur with the carboxylic acid activated as a coenzyme A thioester. The enzyme catalyses three steps in this pathway, also acting on (3R,4R)-3,4-dihydroxycyclohexa-1,5-diene-1-carbonyl-CoA and (5S)-5-hydroxycyclohex-1-ene-1-carbonyl-CoA.
References:
1. Reynolds, K.A., Wang, P., Fox, K.M., Speedie, M.K., Lam, Y. and Floss, H.G. Purification and characterization of a novel enoyl coenzyme A reductase from Streptomyces collinus. J. Bacteriol. 174 (1992) 3850-3854. [PMID: 1597409]
2. Wang, P., Denoya, C.D., Morgenstern, M.R., Skinner, D.D., Wallace, K.K., Digate, R., Patton, S., Banavali, N., Schuler, G., Speedie, M.K. and Reynolds, K.A. Cloning and characterization of the gene encoding 1-cyclohexenylcarbonyl coenzyme A reductase from Streptomyces collinus. J. Bacteriol. 178 (1996) 6873-6881. [PMID: 8955309]
Accepted name: hydrogen peroxide-dependent heme synthase
Reaction: Fe-coproporphyrin III + 2 H2O2 = protoheme + 2 CO2 + 4 H2O (overall reaction)
(1a) Fe-coproporphyrin III + H2O2 = harderoheme III + CO2 + 2 H2O
(1b) harderoheme III + H2O2 = protoheme + CO2 + 2 H2O
For diagram of reaction, click here
Other name(s): coproheme III oxidative decarboxylase; hemQ (gene name)
Systematic name: Fe-coproporphyrin III:hydrogen peroxide oxidoreductase (decarboxylating)
Comments: The enzyme participates in a heme biosynthesis pathway found in Gram-positive bacteria. The initial decarboxylation step is fast and yields the three-propanoate harderoheme isomer III. The second decarboxylation is much slower. cf. EC 1.3.98.6, SAM-dependent heme synthase.
References:
1. Dailey, T.A., Boynton, T.O., Albetel, A.N., Gerdes, S., Johnson, M.K. and Dailey, H.A. Discovery and characterization of HemQ: an essential heme biosynthetic pathway component. J. Biol. Chem 285 (2010) 25978-25986. [PMID: 20543190]
2. Celis, A.I., Streit, B.R., Moraski, G.C., Kant, R., Lash, T.D., Lukat-Rodgers, G.S., Rodgers, K.R. and DuBois, J.L. Unusual peroxide-dependent, heme-transforming reaction catalyzed by HemQ. Biochemistry 54 (2015) 4022-4032. [PMID: 26083961]
3. Hofbauer, S., Mlynek, G., Milazzo, L., Puhringer, D., Maresch, D., Schaffner, I., Furtmuller, P.G., Smulevich, G., Djinovic-Carugo, K. and Obinger, C. Hydrogen peroxide-mediated conversion of coproheme to heme b by HemQ-lessons from the first crystal structure and kinetic studies. FEBS J. 283 (2016) 4386-4401. [PMID: 27758026]
4. Celis, A.I., Gauss, G.H., Streit, B.R., Shisler, K., Moraski, G.C., Rodgers, K.R., Lukat-Rodgers, G.S., Peters, J.W. and DuBois, J.L. Structure-based mechanism for oxidative decarboxylation reactions mediated by amino acids and heme propionates in coproheme decarboxylase (HemQ). J. Am. Chem. Soc. 139 (2017) 1900-1911. [PMID: 27936663]
Accepted name: AdoMet-dependent heme synthase
Reaction: Fe-coproporphyrin III + 2 S-adenosyl-L-methionine = protoheme + 2 CO2 + 2 5'-deoxyadenosine + 2 L-methionine
For diagram of reaction, click here
Other name(s): ahbD (gene name); SAM-dependent heme synthase
Systematic name: Fe-coproporphyrin III:S-adenosyl-L-methionine oxidoreductase (decarboxylating)
Comments: This radical AdoMet enzyme participates in a heme biosynthesis pathway found in archaea and sulfur-reducing bacteria. cf. EC 1.3.98.5, hydrogen peroxide-dependent heme synthase.
References:
1. Bali, S., Lawrence, A.D., Lobo, S.A., Saraiva, L.M., Golding, B.T., Palmer, D.J., Howard, M.J., Ferguson, S.J. and Warren, M.J. Molecular hijacking of siroheme for the synthesis of heme and d1 heme. Proc. Natl Acad. Sci. USA 108 (2011) 18260-18265. [PMID: 21969545]
2. Kuhner, M., Haufschildt, K., Neumann, A., Storbeck, S., Streif, J. and Layer, G. The alternative route to heme in the methanogenic archaeon Methanosarcina barkeri. Archaea 2014 (2014) 327637. [PMID: 24669201]
Accepted name: dissimilatory dimethyldisulfide reductase
Reaction: 2 methanethiol + NAD+ = dimethyl disulfide + NADH + H+
Systematic name: methanethiol:NAD+ oxidoreductase (dimethyl disulfide-forming)
Comments: The enzyme's activity has been demonstrated in the bacterium Thiobacillus thioparus E6. The methanethiol formed is eventually oxidized to sulfate and carbon dioxide, and the latter assimilated for autotrophic growth.
References:
1. Smith, N. A. and Kelly, D. P. Isolation and physiological characterization of authotrophic sulphur bacteria oxidizing dimethyldisulphide as sole source of energy. J. Gen. Microbiol. 134 (1988) 1407-1417.
2. Smith, N. A. and Kelly, D. P. Mechanism of oxidation of dimethyl disulphide by Thiobacillus thioparus E6. J. Gen. Microbiol. 134 (1988) 3031-3039.
Accepted name: hydroxymethylphosphonate dioxygenase
Reaction: (hydroxymethyl)phosphonate + O2 = formate + phosphate
Other name(s): phnZ1 (gene name)
Systematic name: hydroxymethylphosphonate:oxygen 1-oxidoreductase (formate-forming)
Comments: Requires iron(II). The enzyme, characterized from the marine bacterium Gimesia maris, participates in a methylphosphonate degradation pathway. It also has the activity of EC 1.13.11.78, (2-amino-1-hydroxyethyl)phosphonate dioxygenase (glycine-forming).
References:
1. Gama, S.R., Vogt, M., Kalina, T., Hupp, K., Hammerschmidt, F., Pallitsch, K. and Zechel, D.L. An oxidative pathway for microbial utilization of methylphosphonic acid as a phosphate source. ACS Chem. Biol. 14 (2019) 735-741. [PMID: 30810303]
Accepted name: [histone H3]-dimethyl-L-lysine36 demethylase
Reaction: a [histone H3]-N6,N6-dimethyl-L-lysine36 + 2 2-oxoglutarate + 2 O2 = a [histone H3]-L-lysine36 + 2 succinate + 2 formaldehyde + 2 CO2 (overall reaction)
(1a) a [histone H3]-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 = a [histone H3]-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
(1b) a [histone H3]-N6-methyl-L-lysine36 + 2-oxoglutarate + O2 = a [histone H3]-L-lysine36 + succinate + formaldehyde + CO2
Other name(s): KDM2A (gene name); KDM2B (gene name); JHDM1A (gene name); JHDM1B (gene name); JmjC domain-containing histone demethylase 1A; H3-K36-specific demethylase (ambiguous); histone-lysine (H3-K36) demethylase (ambiguous); histone demethylase (ambiguous); protein-6-N,6-N-dimethyl-L-lysine,2-oxoglutarate:oxygen oxidoreductase; protein-N6,N6-dimethyl-L-lysine,2-oxoglutarate:oxygen oxidoreductase; [histone-H3]-lysine36 demethylase
Systematic name: [histone H3]-N6,N6-dimethyl-L-lysine36,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires iron(II). Of the seven potential methylation sites in histones H3 (K4, K9, K27, K36, K79) and H4 (K20, R3) from HeLa cells, the enzyme is specific for Lys36. Lysine residues exist in three methylation states (mono-, di- and trimethylated). The enzyme preferentially demethylates the dimethyl form of Lys36 (K36me2), which is its natural substrate, to form the monomethylated and unmethylated forms of Lys36. It can also demethylate monomethylated (but not the trimethylated) Lys36. cf. EC 1.14.11.69, [histone H3]-trimethyl-L-lysine36 demethylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Tsukada, Y., Fang, J., Erdjument-Bromage, H., Warren, M.E., Borchers, C.H., Tempst, P. and Zhang, Y. Histone demethylation by a family of JmjC domain-containing proteins. Nature 439 (2006) 811-816. [PMID: 16362057]
Accepted name: glutarate dioxygenase
Reaction: glutarate + 2-oxoglutarate + O2 = (S)-2-hydroxyglutarate + succinate + CO2
Other name(s): csiD (gene name)
Systematic name: glutarate, 2-oxoglutarate:oxygen oxidoreductase ((S)-2-hydroxyglutarate-forming)
Comments: Requires iron(II). The enzyme, characterized from the bacteria Escherichia coli and Pseudomonas putida, participates in L-lysine degradation in many bacteria. It provides an alternative route for L-glutarate degradation that does not proceed via CoA-activated intermediates.
References:
1. Knorr, S., Sinn, M., Galetskiy, D., Williams, R.M., Wang, C., Muller, N., Mayans, O., Schleheck, D. and Hartig, J.S. Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate. Nat Commun 9 (2018) 5071. [PMID: 30498244]
2. Zhang, M., Gao, C., Guo, X., Guo, S., Kang, Z., Xiao, D., Yan, J., Tao, F., Zhang, W., Dong, W., Liu, P., Yang, C., Ma, C. and Xu, P. Increased glutarate production by blocking the glutaryl-CoA dehydrogenation pathway and a catabolic pathway involving L-2-hydroxyglutarate. Nat Commun 9 (2018) 2114. [PMID: 29844506]
Accepted name: [histone H3]-dimethyl-L-lysine9 demethylase
Reaction: a [histone H3]-N6,N6-dimethyl-L-lysine9 + 2 2-oxoglutarate + 2 O2 = a [histone H3]-L-lysine9 + 2 succinate + 2 formaldehyde + 2 CO2 (overall reaction)
(1a) a [histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2 = a [histone H3]-N6-methyl-L-lysine9 + succinate + formaldehyde + CO2
(1b) a [histone H3]-N6-methyl-L-lysine9 + 2-oxoglutarate + O2 = a [histone H3]-L-lysine9 + succinate + formaldehyde + CO2
Other name(s): KDM3A (gene name); KDM3B (gene name); JMJD1A (gene name); JMJD1B (gene name); JHDM2A (gene name); JHDM2B (gene name); KDM7B (gene name); PHF8 (gene name); HR (gene name)
Systematic name: [histone H3]-N6,N6-dimethyl-L-lysine-9,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires iron(II). This entry describes a group of enzymes that demethylate N-methylated Lys-9 residues in the tail of the histone protein H3 (H3K9). This lysine residue can exist in three methylation states (mono-, di- and trimethylated), but this group of enzymes only act on the the di- and mono-methylated forms. The enzymes are dioxygenases and act by hydroxylating the methyl group, forming an unstable hemiaminal that leaves as formaldehyde. cf. EC 1.14.11.66, [histone H3]-trimethyl-L-lysine9 demethylase.
References:
1. Yamane, K., Toumazou, C., Tsukada, Y., Erdjument-Bromage, H., Tempst, P., Wong, J. and Zhang, Y. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 125 (2006) 483-495. [PMID: 16603237]
2. Loh, Y.H., Zhang, W., Chen, X., George, J. and Ng, H.H. Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. Genes Dev. 21 (2007) 2545-2557. [PMID: 17938240]
3. Feng, W., Yonezawa, M., Ye, J., Jenuwein, T. and Grummt, I. PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation. Nat. Struct. Mol. Biol. 17 (2010) 445-450. [PMID: 20208542]
4. Kuroki, S., Matoba, S., Akiyoshi, M., Matsumura, Y., Miyachi, H., Mise, N., Abe, K., Ogura, A., Wilhelm, D., Koopman, P., Nozaki, M., Kanai, Y., Shinkai, Y. and Tachibana, M. Epigenetic regulation of mouse sex determination by the histone demethylase Jmjd1a. Science 341 (2013) 1106-1109. [PMID: 24009392]
5. Liu, L., Kim, H., Casta, A., Kobayashi, Y., Shapiro, L.S. and Christiano, A.M. Hairless is a histone H3K9 demethylase. FASEB J. 28 (2014) 1534-1542. [PMID: 24334705]
Accepted name: [histone H3]-trimethyl-L-lysine9 demethylase
Reaction: a [histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2 2-oxoglutarate + 2 O2 = a [histone H3]-N6-methyl-L-lysine9 + 2 succinate + 2 formaldehyde + 2 CO2 (overall reaction)
(1a) a [histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2-oxoglutarate + O2 = a [histone H3]-N6,N6-dimethyl-L-lysine9 + succinate + formaldehyde + CO2
(1b) a [histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2 = a [histone H3]-N6-methyl-L-lysine9 + succinate + formaldehyde + CO2
Other name(s): KDM4A (gene name); KDM4B (gene name); KDM4C (gene name); KDM4D (gene name); JHDM3A (gene name); JMJD2 (gene name); JMJD2A (gene name); GASC1 (gene name)
Systematic name: [histone H3]-N6,N6,N6-trimethyl-L-lysine-9,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires iron(II). This entry describes a group of enzymes that demethylate N-methylated Lys9 residues in the tail of the histone protein H3 (H3K9). This lysine residue can exist in three methylation states (mono-, di- and trimethylated), but this group of enzymes only act on the the tri- and di-methylated forms. The enzymes are dioxygenases and act by hydroxylating the methyl group, forming an unstable hemiaminal that leaves as formaldehyde. cf. EC 1.14.11.65, [histone H3]-dimethyl-L-lysine9 demethylase.
References:
1. Cloos, P.A., Christensen, J., Agger, K., Maiolica, A., Rappsilber, J., Antal, T., Hansen, K.H. and Helin, K. The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 442 (2006) 307-311. [PMID: 16732293]
2. Fodor, B.D., Kubicek, S., Yonezawa, M., O'Sullivan, R.J., Sengupta, R., Perez-Burgos, L., Opravil, S., Mechtler, K., Schotta, G. and Jenuwein, T. Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells. Genes Dev. 20 (2006) 1557-1562. [PMID: 16738407]
3. Klose, R.J., Yamane, K., Bae, Y., Zhang, D., Erdjument-Bromage, H., Tempst, P., Wong, J. and Zhang, Y. The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature 442 (2006) 312-316. [PMID: 16732292]
4. Whetstine, J.R., Nottke, A., Lan, F., Huarte, M., Smolikov, S., Chen, Z., Spooner, E., Li, E., Zhang, G., Colaiacovo, M. and Shi, Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125 (2006) 467-481. [PMID: 16603238]
Accepted name: [histone H3]-trimethyl-L-lysin4 demethylase
Reaction: a [histone H3]-N6,N6,N6-trimethyl-L-lysine4 + 3 2-oxoglutarate + 3 O2 = a [histone H3]-L-lysine4 + 3 succinate + 3 formaldehyde + 3 CO2 (overall reaction)
(1a) a [histone H3]-N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2 = a [histone H3]-N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
(1b) a [histone H3]-N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2 = a [histone H3]-N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
(1c) a [histone H3]-N6-methyl-L-lysine4 + 2-oxoglutarate + O2 = a [histone H3]-L-lysine4 + succinate + formaldehyde + CO2
Other name(s): KDM5A (gene name); KDM5B (gene name); KDM5C (gene name); KDM5D (gene name); JARID1A (gene name)
Systematic name: [histone H3]-N6,N6,N6-trimethyl-L-lysine-4,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires iron(II). This entry describes a group of enzymes that demethylate N-methylated L-lysine residues at position 4 of histone H3 (H3K4). The enzymes are dioxygenases and act by hydroxylating the methyl group, forming an unstable hemiaminal that leaves as formaldehyde. They can act on tri-, di-, and mono-methylated forms.
References:
1. Seward, D.J., Cubberley, G., Kim, S., Schonewald, M., Zhang, L., Tripet, B. and Bentley, D.L. Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins. Nat. Struct. Mol. Biol. 14 (2007) 240-242. [PMID: 17310255]
2. Klose, R.J., Yan, Q., Tothova, Z., Yamane, K., Erdjument-Bromage, H., Tempst, P., Gilliland, D.G., Zhang, Y. and Kaelin, W.G., Jr. The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell 128 (2007) 889-900. [PMID: 17320163]
3. Iwase, S., Lan, F., Bayliss, P., de la Torre-Ubieta, L., Huarte, M., Qi, H.H., Whetstine, J.R., Bonni, A., Roberts, T.M. and Shi, Y. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 128 (2007) 1077-1088. [PMID: 17320160]
4. Christensen, J., Agger, K., Cloos, P.A., Pasini, D., Rose, S., Sennels, L., Rappsilber, J., Hansen, K.H., Salcini, A.E. and Helin, K. RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Cell 128 (2007) 1063-1076. [PMID: 17320161]
Accepted name: [histone H3]-trimethyl-L-lysine27 demethylase
Reaction: a [histone H3]-N6,N6,N6-trimethyl-L-lysine27 + 2 2-oxoglutarate + 2 O2 = a [histone H3]-N6-methyl-L-lysine27 + 2 succinate + 2 formaldehyde + 2 CO2 (overall reaction)
(1a) a [histone H3]-N6,N6,N6-trimethyl-L-lysine27 + 2-oxoglutarate + O2 = a [histone H3]-N6,N6-dimethyl-L-lysine27 + succinate + formaldehyde + CO2
(1b) a [histone H3]-N6,N6-dimethyl-L-lysine27 + 2-oxoglutarate + O2 = a [histone H3]-N6-methyl-L-lysine27 + succinate + formaldehyde + CO2
Other name(s): KDM6A (gene name); KDM6C (gene name); UTX (gene name); UTY (gene name); JMJD3 (gene name)
Systematic name: [histone H3]-N6,N6,N6-trimethyl-L-lysine-27,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires iron(II). This entry describes a group of enzymes that demethylate N-methylated L-lysine residues at position 27 of histone H3 (H3K27). The enzymes are dioxygenases and act by hydroxylating the methyl group, forming an unstable hemiaminal that leaves as formaldehyde. They can act on tri- and di-methylated forms, but have no activity with the mono-methylated form.
References:
1. De Santa, F., Totaro, M.G., Prosperini, E., Notarbartolo, S., Testa, G. and Natoli, G. The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing. Cell 130 (2007) 1083-1094. [PMID: 17825402]
2. Hong, S., Cho, Y.W., Yu, L.R., Yu, H., Veenstra, T.D. and Ge, K. Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases. Proc. Natl Acad. Sci. USA 104 (2007) 18439-18444. [PMID: 18003914]
3. Lan, F., Bayliss, P.E., Rinn, J.L., Whetstine, J.R., Wang, J.K., Chen, S., Iwase, S., Alpatov, R., Issaeva, I., Canaani, E., Roberts, T.M., Chang, H.Y. and Shi, Y. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 449 (2007) 689-694. [PMID: 17851529]
4. Lee, M.G., Villa, R., Trojer, P., Norman, J., Yan, K.P., Reinberg, D., Di Croce, L. and Shiekhattar, R. Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination. Science 318 (2007) 447-450. [PMID: 17761849]
5. Xiang, Y., Zhu, Z., Han, G., Lin, H., Xu, L. and Chen, C.D. JMJD3 is a histone H3K27 demethylase. Cell Res 17 (2007) 850-857. [PMID: 17923864]
Accepted name: [histone H3]-trimethyl-L-lysine36 demethylase
Reaction: a [histone H3]-N6,N6,N6-trimethyl-L-lysine36 + 2 2-oxoglutarate + 2 O2 = a [histone H3]-N6-methyl-L-lysine36 + 2 succinate + 2 formaldehyde + 2 CO2 (overall reaction)
(1a) a [histone H3]-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2 = a [histone H3]-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
(1b) a [histone H3]-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 = a [histone H3]-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
Other name(s): KDM4A (gene name); KDM4B (gene name); RPH1 (gene name); JHDM3A (gene name); JHDM3B (gene name); JMJD2A (gene name); JMJD2B (gene name)
Systematic name: [histone H3]-N6,N6,N6-trimethyl-L-lysine-36,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires iron(II). This entry describes a group of enzymes that demethylate N-methylated Lys36 residues in the tail of the histone protein H3 (H3K36). This lysine residue can exist in three methylation states (mono-, di- and trimethylated), but this group of enzymes only act on the the tri- and di-methylated forms. The enzymes are dioxygenases and act by hydroxylating the methyl group, forming an unstable hemiaminal that leaves as formaldehyde. Since trimethylation of H3K36 enhances transcription, this enzyme acts as a transcription repressor. The enzymes that possess this activity often also catalyse the activity of EC 1.14.11.66, [histone H3]-trimethyl-L-lysine9 demethylase. cf. EC 1.14.11.27, [histone H3]-dimethyl-L-lysine36 demethylase.
References:
1. Whetstine, J.R., Nottke, A., Lan, F., Huarte, M., Smolikov, S., Chen, Z., Spooner, E., Li, E., Zhang, G., Colaiacovo, M. and Shi, Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125 (2006) 467-481. [PMID: 16603238]
2. Klose, R.J., Yamane, K., Bae, Y., Zhang, D., Erdjument-Bromage, H., Tempst, P., Wong, J. and Zhang, Y. The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature 442 (2006) 312-316. [PMID: 16732292]
3. Kim, T. and Buratowski, S. Two Saccharomyces cerevisiae JmjC domain proteins demethylate histone H3 Lys36 in transcribed regions to promote elongation. J. Biol. Chem 282 (2007) 20827-20835. [PMID: 17525156]
4. Couture, J.F., Collazo, E., Ortiz-Tello, P.A., Brunzelle, J.S. and Trievel, R.C. Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase. Nat. Struct. Mol. Biol. 14 (2007) 689-695. [PMID: 17589523]
5. Lin, C.H., Li, B., Swanson, S., Zhang, Y., Florens, L., Washburn, M.P., Abmayr, S.M. and Workman, J.L. Heterochromatin protein 1a stimulates histone H3 lysine 36 demethylation by the Drosophila KDM4A demethylase. Mol. Cell 32 (2008) 696-706. [PMID: 19061644]
6. Colmenares, S.U., Swenson, J.M., Langley, S.A., Kennedy, C., Costes, S.V. and Karpen, G.H. Drosophila Histone Demethylase KDM4A Has Enzymatic and Non-enzymatic Roles in Controlling Heterochromatin Integrity. Dev Cell 42 (2017) 156-169.e5. [PMID: 28743002]
Accepted name: [histone-H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase
Reaction: a [histone H3]-N6,N6-dimethyl-L-lysine4 + 2 acceptor + 2 H2O = a [histone H3]-L-lysine4 + 2 formaldehyde + 2 reduced acceptor (overall reaction)
(1a) a [histone H3]-N6,N6-dimethyl-L-lysine4 + acceptor + H2O = a [histone H3]-N6-methyl-L-lysine4 + formaldehyde + reduced acceptor
(1b) a [histone H3]-N6-methyl-L-lysine4 + acceptor + H2O = a [histone H3]-L-lysine4 + formaldehyde + reduced acceptor
Other name(s): KDM1 (gene name); LSD1 (gene name); lysine-specific histone demethylase 1
Systematic name: [histone-H3]-N6,N6-dimethyl-L-lysine-4:acceptor oxidoreductase (demethylating)
Comments: The enzyme specifically removes methyl groups from mono- and dimethylated lysine4 of histone 3. During the reaction the substrate is oxidized by the FAD cofactor of the enzyme to generate the corresponding imine, which is subsequently hydrolysed in the form of formaldehyde.The enzyme is similar to flavin amine oxidases, and differs from all other known histone lysine demethylases, which are iron(II)- and 2-oxoglutarate-dependent dioxygenases. The physiological electron acceptor is not known with certainty. In vitro the enzyme can use oxygen, which is reduced to hydrogen peroxide, but generation of hydrogen peroxide in the chromatin environment is unlikely as it will result in oxidative damage of DNA.
References:
1. Forneris, F., Binda, C., Vanoni, M.A., Mattevi, A. and Battaglioli, E. Histone demethylation catalysed by LSD1 is a flavin-dependent oxidative process. FEBS Lett. 579 (2005) 2203-2207. [PMID: 15811342]
2. Forneris, F., Battaglioli, E., Mattevi, A. and Binda, C. New roles of flavoproteins in molecular cell biology: histone demethylase LSD1 and chromatin. FEBS J. 276 (2009) 4304-4312. [PMID: 19624733]
[EC 2.1.1.43 Transferred entry: histone-lysine N-methyltransferase. Now described by EC 2.1.1.354, histone H3 lysine4 N-trimethyltransferase; EC 2.1.1.355, histone H3 lysine9 N-trimethyltransferase; EC 2.1.1.356, histone H3 lysine27 N-trimethyltransferase; EC 2.1.1.357, histone H3 lysine36 N-dimethyltransferase; EC 2.1.1.358, histone H3 dimethyl-L-lysine36 N-methyltransferase; EC 2.1.1.359, histone H3 lysine36 N-trimethyltransferase; EC 2.1.1.360, histone H3 lysine79 N-trimethyltransferase; EC 2.1.1.361, histone H4 lysine20 N-methyltransferase, and EC 2.1.1.362, histone H4 N-methyl-L-lysine20 N-methyltransferase. (EC 2.1.1.43 created 1976, modified 1982, modified 1983, deleted 2019)]
Accepted name: tocopherol C-methyltransferase
Reaction: (1) S-adenosyl-L-methionine + γ-tocopherol = S-adenosyl-L-homocysteine + α-tocopherol
(2) S-adenosyl-L-methionine + δ-tocopherol = S-adenosyl-L-homocysteine + β-tocopherol
(3) S-adenosyl-L-methionine + γ-tocotrienol = S-adenosyl-L-homocysteine + α-tocotrienol
(4) S-adenosyl-L-methionine + δ-tocotrienol = S-adenosyl-L-homocysteine + β-tocotrienol
For diagram of reaction, click here or click here
Other name(s): γ-tocopherol methyltransferase; VTE4 (gene name); S-adenosyl-L-methionine:γ-tocopherol 5-O-methyltransferase (incorrect); tocopherol O-methyltransferase (incorrect)
Systematic name: S-adenosyl-L-methionine:γ-tocopherol 5-C-methyltransferase
Comments: The enzymes from plants and photosynthetic bacteria have similar efficiency with the γ and δ isomers of tocopherols and tocotrienols.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 84788-82-9
References:
1. Camara, B. and D'Harlingue, A. Demonstration and solubilization of S-adenosylmethionine: γ-tocopherol methyltransferase from Capsicum chromoplasts. Plant Cell Rep. 4 (1985) 31-32. [PMID: 24253640]
2. Koch, M., Lemke, R., Heise, K.P. and Mock, H.P. Characterization of γ-tocopherol methyltransferases from Capsicum annuum L and Arabidopsis thaliana. Eur. J. Biochem. 270 (2003) 84-92. [PMID: 12492478]
3. Zhang, G.Y., Liu, R.R., Xu, G., Zhang, P., Li, Y., Tang, K.X., Liang, G.H. and Liu, Q.Q. Increased α-tocotrienol content in seeds of transgenic rice overexpressing Arabidopsis γ-tocopherol methyltransferase. Transgenic Res. 22 (2013) 89-99. [PMID: 22763462]
Accepted name: cycloartenol 24-C-methyltransferase
Reaction: S-adenosyl-L-methionine + cycloartenol = S-adenosyl-L-homocysteine + cyclolaudenol
For diagram of reaction, click here
Glossary: cyclolaudenol = (24S)-24-methylcycloart-25-en-3β-ol
Other name(s): sterol C-methyltransferase
Systematic name: S-adenosyl-L-methionine:cycloartenol 24-C-methyltransferase
Comments: S-Adenosyl-L-methionine methylates the Si face of the 24(25)-double bond with elimination of a hydrogen atom from the pro-Z methyl group at C-25.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 50936-46-4
References:
1. Mangla, A.T. and Nes, W.D. Sterol C-methyl transferase from Prototheca wickerhamii mechanism, sterol specificity and inhibition. Bioorg. Med. Chem. 8 (2000) 925. [PMID: 10882005]
Accepted name: histone H3 lysine-4 N-trimethyltransferase
Reaction: 3 S-adenosyl-L-methionine + a [histone H3]-L-lysine4 = 3 S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine4 (overall reaction)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine4 = S-adenosyl-L-homocysteine + a [histone H3]-N6-methyl-L-lysine4
(1b) S-adenosyl-L-methionine + a [histone H3]-N6-methyl-L-lysine4 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6-dimethyl-L-lysine4
(1c) S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine4 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine4
Other name(s): KMT2A (gene name); KMT2B (gene name); KMT2C (gene name); KMT2D (gene name); KMT2E (gene name); KMT2F (gene name); KMT2G (gene name); KMT2H (gene name); KMT3C (gene name); KMT3D (gene name); KMT3E (gene name); KMT7 (gene name); PRDM7 (gene name); PRDM9 (gene name); MLL1 (gene name); MLL2 (gene name); MLL3 (gene name); MLL4 (gene name); MLL5 (gene name); SETD1A (gene name); ASH1L (gene name); SMYD1 (gene name); SMYD2 (gene name); SMYD3 (gene name); SET7/9 (gene name)
Systematic name: S-adenosyl-L-methionine:[histone H3]-L-lysine4 N6-methyltransferase
Comments: This entry describes several enzymes that successively methylate the L-lysine4 residue of histone H3 (H3K4), ultimately generating a trimethylated form. These modifications influence the binding of chromatin-associated proteins. In most cases the trimethylation of this position is associated with gene activation. Unlike the other enzymes, KMT7 catalyses only monomethylation.
References:
1. Nakamura, T., Mori, T., Tada, S., Krajewski, W., Rozovskaia, T., Wassell, R., Dubois, G., Mazo, A., Croce, C.M. and Canaani, E. ALL-1 is a histone methyltransferase that assembles a supercomplex of proteins involved in transcriptional regulation. Mol. Cell 10 (2002) 1119-1128. [PMID: 12453419]
2. Xiao, B., Jing, C., Wilson, J.R., Walker, P.A., Vasisht, N., Kelly, G., Howell, S., Taylor, I.A., Blackburn, G.M. and Gamblin, S.J. Structure and catalytic mechanism of the human histone methyltransferase SET7/9. Nature 421 (2003) 652-656. [PMID: 12540855]
3. Hamamoto, R., Furukawa, Y., Morita, M., Iimura, Y., Silva, F.P., Li, M., Yagyu, R. and Nakamura, Y. SMYD3 encodes a histone methyltransferase involved in the proliferation of cancer cells. Nat. Cell Biol. 6 (2004) 731-740. [PMID: 15235609]
4. Blazer, L.L., Lima-Fernandes, E., Gibson, E., Eram, M.S., Loppnau, P., Arrowsmith, C.H., Schapira, M. and Vedadi, M. PR domain-containing protein 7 (PRDM7) is a histone 3 lysine 4 trimethyltransferase. J. Biol. Chem 291 (2016) 13509-13519. [PMID: 27129774]
Accepted name: histone H3 lysine-9 N-trimethyltransferase
Reaction: 3 S-adenosyl-L-methionine + a [histone H3]-L-lysine9 = 3 S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine9 (overall reaction)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine9 = S-adenosyl-L-homocysteine + a [histone H3]-N6-methyl-L-lysine9
(1b) S-adenosyl-L-methionine + a [histone H3]-N6-methyl-L-lysine9 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6-dimethyl-L-lysine9
(1c) S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine9 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine9
Other name(s): KMT1A (gene name); KMT1B (gene name); KMT1C (gene name); KMT1D (gene name); KMT1E (gene name); KMT1F (gene name); MT8 (gene name); SUV39H1 (gene name); G9A (gene name); EHMT1 (gene name); PRDM2 (gene name)
Systematic name: S-adenosyl-L-methionine:[histone H3]-L-lysine9 N6-methyltransferase
Comments: This entry describes several enzymes that successively methylate the L-lysine9 residue of histone H3 (H3K9), ultimately generating a trimethylated form. These modifications influence the binding of chromatin-associated proteins. In general, the methylation of H3K9 leads to transcriptional repression of the affected target genes.
References:
1. O'Carroll, D., Scherthan, H., Peters, A.H., Opravil, S., Haynes, A.R., Laible, G., Rea, S., Schmid, M., Lebersorger, A., Jerratsch, M., Sattler, L., Mattei, M.G., Denny, P., Brown, S.D., Schweizer, D. and Jenuwein, T. Isolation and characterization of Suv39h2, a second histone H3 methyltransferase gene that displays testis-specific expression. Mol. Cell Biol. 20 (2000) 9423-9433. [PMID: 11094092]
2. Schotta, G., Ebert, A., Krauss, V., Fischer, A., Hoffmann, J., Rea, S., Jenuwein, T., Dorn, R. and Reuter, G. Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing. EMBO J. 21 (2002) 1121-1131. [PMID: 11867540]
3. Tachibana, M., Sugimoto, K., Nozaki, M., Ueda, J., Ohta, T., Ohki, M., Fukuda, M., Takeda, N., Niida, H., Kato, H. and Shinkai, Y. G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. Genes Dev. 16 (2002) 1779-1791. [PMID: 12130538]
4. Schultz, D.C., Ayyanathan, K., Negorev, D., Maul, G.G. and Rauscher, F.J., 3rd. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev. 16 (2002) 919-932. [PMID: 11959841]
5. Kim, K.C., Geng, L. and Huang, S. Inactivation of a histone methyltransferase by mutations in human cancers. Cancer Res. 63 (2003) 7619-7623. [PMID: 14633678]
6. Wu, H., Min, J., Lunin, V.V., Antoshenko, T., Dombrovski, L., Zeng, H., Allali-Hassani, A., Campagna-Slater, V., Vedadi, M., Arrowsmith, C.H., Plotnikov, A.N. and Schapira, M. Structural biology of human H3K9 methyltransferases. PLoS One 5 (2010) e8570. [PMID: 20084102]
Accepted name: histone H3 lysine27 N-trimethyltransferase
Reaction: 3 S-adenosyl-L-methionine + a [histone H3]-L-lysine27 = 3 S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine27 (overall reaction)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine27 = S-adenosyl-L-homocysteine + a [histone H3]-N6-methyl-L-lysine27
(1b) S-adenosyl-L-methionine + a [histone H3]-N6-methyl-L-lysine27 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6-dimethyl-L-lysine27
(1c) S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine27 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine27
Other name(s): KMT6A (gene name); KMT6B (gene name); EZH1 (gene name); EZH2 (gene name)
Systematic name: S-adenosyl-L-methionine:[histone H3]-L-lysine27 N6-methyltransferase
Comments: This entry describes enzymes that successively methylate the L-lysine27 residue of histone H3 (H3K27), ultimately generating a trimethylated form. These modifications influence the binding of chromatin-associated proteins. The methylation of lysine27 leads to transcriptional repression of the affected target genes. The enzyme associates with other proteins to form a complex that is essential for activity. The enzyme can also methylate some non-histone proteins.
References:
1. Cao, R., Wang, L., Wang, H., Xia, L., Erdjument-Bromage, H., Tempst, P., Jones, R.S. and Zhang, Y. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298 (2002) 1039-1043. [PMID: 12351676]
2. Kuzmichev, A., Nishioka, K., Erdjument-Bromage, H., Tempst, P. and Reinberg, D. Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 16 (2002) 2893-2905. [PMID: 12435631]
3. Kirmizis, A., Bartley, S.M., Kuzmichev, A., Margueron, R., Reinberg, D., Green, R. and Farnham, P.J. Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev. 18 (2004) 1592-1605. [PMID: 15231737]
4. Schlesinger, Y., Straussman, R., Keshet, I., Farkash, S., Hecht, M., Zimmerman, J., Eden, E., Yakhini, Z., Ben-Shushan, E., Reubinoff, B.E., Bergman, Y., Simon, I. and Cedar, H. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat. Genet. 39 (2007) 232-236. [PMID: 17200670]
5. Shen, X., Liu, Y., Hsu, Y.J., Fujiwara, Y., Kim, J., Mao, X., Yuan, G.C. and Orkin, S.H. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Mol. Cell 32 (2008) 491-502. [PMID: 19026780]
6. Ezhkova, E., Lien, W.H., Stokes, N., Pasolli, H.A., Silva, J.M. and Fuchs, E. EZH1 and EZH2 cogovern histone H3K27 trimethylation and are essential for hair follicle homeostasis and wound repair. Genes Dev. 25 (2011) 485-498. [PMID: 21317239]
Accepted name: histone H3 lysine36 N-dimethyltransferase
Reaction: 2 S-adenosyl-L-methionine + a [histone H3]-L-lysine36 = 2 S-adenosyl-L-homocysteine + a [histone H3]-N6,N6-dimethyl-L-lysine36 (overall reaction)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine36 = S-adenosyl-L-homocysteine + a [histone H3]-N6-methyl-L-lysine36
(1b) S-adenosyl-L-methionine + a [histone H3]-N6-methyl-L-lysine36 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6-dimethyl-L-lysine36
Other name(s): KMT3B (gene name); KMT3C (gene name); NSD2 (gene name); NSD3 (gene name); SETMAR (gene name); WHSC1 (gene name)
Systematic name: S-adenosyl-L-methionine:[histone H3]-L-lysine36 N6-dimethyltransferase
Comments: This entry describes a group of metazoan enzymes that catalyse two successive methylations of lysine 36 of histone H3 (H3K36), forming mono- and dimethylated forms. These modifications influence the binding of chromatin-associated proteins. The product can be further methylated to the trimethyl form by EC 2.1.1.358, histone H3 dimethyl-L-lysine36 N-methyltransferase. The yeast SET2 enzyme can catalyse all three methylations (see EC 2.1.1.359, histone H3 lysine36 N-trimethyltransferase).
References:
1. Fnu, S., Williamson, E.A., De Haro, L.P., Brenneman, M., Wray, J., Shaheen, M., Radhakrishnan, K., Lee, S.H., Nickoloff, J.A. and Hromas, R. Methylation of histone H3 lysine 36 enhances DNA repair by nonhomologous end-joining. Proc. Natl Acad. Sci. USA 108 (2011) 540-545. [PMID: 21187428]
2. Kuo, A.J., Cheung, P., Chen, K., Zee, B.M., Kioi, M., Lauring, J., Xi, Y., Park, B.H., Shi, X., Garcia, B.A., Li, W. and Gozani, O. NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming. Mol. Cell 44 (2011) 609-620. [PMID: 22099308]
3. Qiao, Q., Li, Y., Chen, Z., Wang, M., Reinberg, D. and Xu, R.M. The structure of NSD1 reveals an autoregulatory mechanism underlying histone H3K36 methylation. J. Biol. Chem 286 (2011) 8361-8368. [PMID: 21196496]
4. Wagner, E.J. and Carpenter, P.B. Understanding the language of Lys36 methylation at histone H3. Nat. Rev. Mol. Cell. Biol. 13 (2012) 115-126. [PMID: 22266761]
Accepted name: histone H3 dimethyl-L-lysine36 N-methyltransferase
Reaction: S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine36 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine36
Other name(s): KMT3A (gene name); SETD2 (gene name)
Systematic name: S-adenosyl-L-methionine:[histone H3]-N6,N6-dimethyl-L-lysine36 N6-methyltransferase
Comments: The enzyme, found in metazoa, methylates a dimethylated L-lysine36 residue of histone H3 (H3K36), which has been methylated previously by EC 2.1.1.357, histone H3 lysine36 N-dimethyltransferase. The homologous enzyme from yeast catalyses all three methylations (see EC 2.1.1.359, histone H3 lysine36 N-trimethyltransferase).
References:
1. Kizer, K.O., Phatnani, H.P., Shibata, Y., Hall, H., Greenleaf, A.L. and Strahl, B.D. A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. Mol. Cell Biol. 25 (2005) 3305-3316. [PMID: 15798214]
2. Yuan, W., Xie, J., Long, C., Erdjument-Bromage, H., Ding, X., Zheng, Y., Tempst, P., Chen, S., Zhu, B. and Reinberg, D. Heterogeneous nuclear ribonucleoprotein L Is a subunit of human KMT3a/Set2 complex required for H3 Lys-36 trimethylation activity in vivo. J. Biol. Chem 284 (2009) 15701-15707. [PMID: 19332550]
3. Wagner, E.J. and Carpenter, P.B. Understanding the language of Lys36 methylation at histone H3. Nat. Rev. Mol. Cell. Biol. 13 (2012) 115-126. [PMID: 22266761]
Accepted name: histone H3 lysine36 N-trimethyltransferase
Reaction: 3 S-adenosyl-L-methionine + a [histone H3]-L-lysine36 = 3 S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine36 (overall reaction)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine36 = S-adenosyl-L-homocysteine + a [histone H3]-N6-methyl-L-lysine36
(1b) S-adenosyl-L-methionine + a [histone H3]-N6-methyl-L-lysine36 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6-dimethyl-L-lysine36
(1c) S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine36 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine36
Other name(s): SET2 (gene name)
Systematic name: S-adenosyl-L-methionine:[histone H3]-L-lysine36 N6-trimethyltransferase
Comments: The enzyme, characterized from yeast, catalyses the successive methylation of lysine36 of histone H3 (H3K36), forming the trimethylated form. These modifications influence the binding of chromatin-associated proteins. The enzyme couples the methylation reactions with transcriptional elongation through an interaction with the large subunit of RNA polymerase II. In mammals this activity is catalysed by two different enzymes, EC 2.1.1.357, histone H3 lysine36 N-dimethyltransferase and EC 2.1.1.358, histone H3 dimethyl-L-lysine36 N-methyltransferase.
References:
1. Strahl, B.D., Grant, P.A., Briggs, S.D., Sun, Z.W., Bone, J.R., Caldwell, J.A., Mollah, S., Cook, R.G., Shabanowitz, J., Hunt, D.F. and Allis, C.D. Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol. Cell Biol. 22 (2002) 1298-1306. [PMID: 11839797]
2. Landry, J., Sutton, A., Hesman, T., Min, J., Xu, R.M., Johnston, M. and Sternglanz, R. Set2-catalyzed methylation of histone H3 represses basal expression of GAL4 in Saccharomyces cerevisiae. Mol. Cell Biol. 23 (2003) 5972-5978. [PMID: 12917322]
3. Morris, S.A., Shibata, Y., Noma, K., Tsukamoto, Y., Warren, E., Temple, B., Grewal, S.I. and Strahl, B.D. Histone H3 K36 methylation is associated with transcription elongation in Schizosaccharomyces pombe. Eukaryot Cell 4 (2005) 1446-1454. [PMID: 16087749]
4. Lin, L.J., Minard, L.V., Johnston, G.C., Singer, R.A. and Schultz, M.C. Asf1 can promote trimethylation of H3 K36 by Set2. Mol. Cell Biol. 30 (2010) 1116-1129. [PMID: 20048053]
Accepted name: histone H3 lysine79 N-trimethyltransferase
Reaction: 3 S-adenosyl-L-methionine + a [histone H3]-L-lysine79 = 3 S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine79 (overall reaction)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine79 = S-adenosyl-L-homocysteine + a [histone H3]-N6-methyl-L-lysine79
(1b) S-adenosyl-L-methionine + a [histone H3]-N6-methyl-L-lysine79 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6-dimethyl-L-lysine79
(1c) S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine79 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine-79
Other name(s): DOT1L (gene name); KMT4 (gene name)
Systematic name: S-adenosyl-L-methionine:[histone H3]-L-lysine79 N6-trimethyltransferase
Comments: The enzyme successively methylates the L-lysine79 residue of histone H3 (H3K79), ultimately generating a trimethylated form. These modifications influence the binding of chromatin-associated proteins. This is the only known methylation event of a lysine residue within the core region of a histone, as all other such modifications occur at the tail.
References:
1. Feng, Q., Wang, H., Ng, H.H., Erdjument-Bromage, H., Tempst, P., Struhl, K. and Zhang, Y. Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr. Biol. 12 (2002) 1052-1058. [PMID: 12123582]
2. Ng, H.H., Feng, Q., Wang, H., Erdjument-Bromage, H., Tempst, P., Zhang, Y. and Struhl, K. Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes Dev. 16 (2002) 1518-1527. [PMID: 12080090]
3. Min, J., Feng, Q., Li, Z., Zhang, Y. and Xu, R.M. Structure of the catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase. Cell 112 (2003) 711-723. [PMID: 12628190]
4. Steger, D.J., Lefterova, M.I., Ying, L., Stonestrom, A.J., Schupp, M., Zhuo, D., Vakoc, A.L., Kim, J.E., Chen, J., Lazar, M.A., Blobel, G.A. and Vakoc, C.R. DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells. Mol. Cell Biol. 28 (2008) 2825-2839. [PMID: 18285465]
Accepted name: histone H4 lysine20 N-methyltransferase
Reaction: S-adenosyl-L-methionine + a [histone H4]-L-lysine20 = S-adenosyl-L-homocysteine + a [histone H4]-N6-methyl-L-lysine-20
Other name(s): KMT5A (gene name); SET8 (gene name); PR-SET7 (gene name)
Systematic name: S-adenosyl-L-methionine:[histone H4]-L-lysine20 N6-methyltransferase
Comments: The enzyme catalyses the monomethylation of the L-lysine20 residue of histone H4 (H4K20). This event is usually followed by further methylation by EC 2.1.1.362, histone H4 N-methyl-L-lysine20 N-methyltransferase. This enzyme plays a pivotal role in DNA replication. Activity is high during the G2 and M phases, but declines significantly during G1 and S phases. Mutations in the enzyme have severe consequences, including DNA double-strand breaks, activation of DNA damage checkpoints, defective cell cycle progression, and reduced cell proliferation.
References:
1. Fang, J., Feng, Q., Ketel, C.S., Wang, H., Cao, R., Xia, L., Erdjument-Bromage, H., Tempst, P., Simon, J.A. and Zhang, Y. Purification and functional characterization of SET8, a nucleosomal histone H4-lysine 20-specific methyltransferase. Curr. Biol. 12 (2002) 1086-1099. [PMID: 12121615]
2. Nishioka, K., Rice, J.C., Sarma, K., Erdjument-Bromage, H., Werner, J., Wang, Y., Chuikov, S., Valenzuela, P., Tempst, P., Steward, R., Lis, J.T., Allis, C.D. and Reinberg, D. PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Mol. Cell 9 (2002) 1201-1213. [PMID: 12086618]
3. Jorgensen, S., Elvers, I., Trelle, M.B., Menzel, T., Eskildsen, M., Jensen, O.N., Helleday, T., Helin, K. and Sorensen, C.S. The histone methyltransferase SET8 is required for S-phase progression. J. Cell Biol. 179 (2007) 1337-1345. [PMID: 18166648]
4. Oda, H., Okamoto, I., Murphy, N., Chu, J., Price, S.M., Shen, M.M., Torres-Padilla, M.E., Heard, E. and Reinberg, D. Monomethylation of histone H4-lysine 20 is involved in chromosome structure and stability and is essential for mouse development. Mol. Cell Biol. 29 (2009) 2278-2295. [PMID: 19223465]
5. Jorgensen, S., Schotta, G. and Sorensen, C.S. Histone H4 lysine 20 methylation: key player in epigenetic regulation of genomic integrity. Nucleic Acids Res. 41 (2013) 2797-2806. [PMID: 23345616]
Accepted name: histone H4 N-methyl-L-lysine20 N-methyltransferase
Reaction: S-adenosyl-L-methionine + a [histone H4]-N6-methyl-L-lysine20 = S-adenosyl-L-homocysteine + a [histone H4]-N6,N6-dimethyl-L-lysine20
Other name(s): KMT5B (gene name); KMT5C (gene name); SUV420H1 (gene name); SUV420H2 (gene name)
Systematic name: S-adenosyl-L-methionine:[histone H4]-N6-methyl-L-lysine20 N6-methyltransferase
Comments: This entry describes a group of enzymes that catalyse a single methylation of monomethylated lysine 20 of histone H4 (H4K20m1, generated by EC 2.1.1.361, histone H4 lysine20 N-methyltransferase), forming the dimethylated form. This modification is broadly distributed across the genome and is likely important for general chromatin-mediated processes. The double-methylated form of lysine20 in histone H4 is the most abundant methylation state of this residue and is found on ~80% of all histone H4 molecules. Full activity of the enzyme requires that the lysine at position 9 of histone H3 is trimethylated.
References:
1. Schotta, G., Lachner, M., Sarma, K., Ebert, A., Sengupta, R., Reuter, G., Reinberg, D. and Jenuwein, T. A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev. 18 (2004) 1251-1262. [PMID: 15145825]
2. Jorgensen, S., Schotta, G. and Sorensen, C.S. Histone H4 lysine 20 methylation: key player in epigenetic regulation of genomic integrity. Nucleic Acids Res. 41 (2013) 2797-2806. [PMID: 23345616]
3. Wu, H., Siarheyeva, A., Zeng, H., Lam, R., Dong, A., Wu, X.H., Li, Y., Schapira, M., Vedadi, M. and Min, J. Crystal structures of the human histone H4K20 methyltransferases SUV420H1 and SUV420H2. FEBS Lett. 587 (2013) 3859-3868. [PMID: 24396869]
4. Southall, S.M., Cronin, N.B. and Wilson, J.R. A novel route to product specificity in the Suv4-20 family of histone H4K20 methyltransferases. Nucleic Acids Res. 42 (2014) 661-671. [PMID: 24049080]
5. Weirich, S., Kudithipudi, S. and Jeltsch, A. Specificity of the SUV4-20H1 and SUV4-20H2 protein lysine methyltransferases and methylation of novel substrates. J. Mol. Biol. 428 (2016) 2344-2358. [PMID: 27105552]
Accepted name: 2-O-sulfo trehalose long-chain-acyltransferase
Reaction: (1) stearoyl-CoA + 2-O-sulfo-α,α-trehalose = 2-O-sulfo-2'-stearoyl-α,α-trehalose + CoA
(2) palmitoyl-CoA + 2-O-sulfo-α,α-trehalose = 2-O-sulfo-2'-palmitoyl-α,α-trehalose + CoA
Other name(s): papA2 (gene name)
Systematic name: acyl-CoA:2-O-sulfo-α,α-trehalose 2'-long-chain-acyltransferase
Comments: This mycobacterial enzyme catalyses the acylation of 2-O-sulfo-α,α-trehalose at the 2' position by a C16 or C18 fatty acyl group during the biosynthesis of mycobacterial sulfolipids.
References:
1. Kumar, P., Schelle, M.W., Jain, M., Lin, F.L., Petzold, C.J., Leavell, M.D., Leary, J.A., Cox, J.S. and Bertozzi, C.R. PapA1 and PapA2 are acyltransferases essential for the biosynthesis of the Mycobacterium tuberculosis virulence factor sulfolipid-1. Proc. Natl Acad. Sci. USA 104 (2007) 11221-11226. [PMID: 17592143]
2. Seeliger, J.C., Holsclaw, C.M., Schelle, M.W., Botyanszki, Z., Gilmore, S.A., Tully, S.E., Niederweis, M., Cravatt, B.F., Leary, J.A. and Bertozzi, C.R. Elucidation and chemical modulation of sulfolipid-1 biosynthesis in Mycobacterium tuberculosis. J. Biol. Chem 287 (2012) 7990-8000. [PMID: 22194604]
Accepted name: aureothin polyketide synthase system
Reaction: 4-nitrobenzoyl-CoA + malonyl-CoA + 4 (S)-methylmalonyl-CoA + 4 NADPH + 4 H+ = demethylluteothin + 5 CO2 + 6 CoA + 4 NADP+ + 3 H2O
For diagram of reaction, click here
Glossary: demethylluteothin = nordeoxyaureothin = 2-[(3E,5E)-3,5-dimethyl-6-(4-nitrophenyl)hexa-3,5-dien-1-yl]-6-hydroxy-3,5-dimethyl-4H-pyran-4-one
aureothin = 2-methoxy-3,5-dimethyl-6-[(2R,4Z)-4-[(2E)-2-methyl-3-(4-nitrophenyl)prop-2-en-1-ylidene]oxolan-2-yl]-4H-pyran-4-one
Other name(s): aurABC (gene names); aureothin polyketide synthase complex
Systematic name: malonyl-CoA/(S)-methylmalonyl-CoA:4-nitrobenzoyl-CoA (methyl)malonyltransferase (demethylluteothin-forming)
Comments: This polyketide synthase, characterized from the bacterium Streptomyces thioluteus, generates the backbone of the antibiotic aureothin. It is composed of 4 modules that total 18 domains and is encoded by three genes. The enzyme accepts the unusual starter unit 4-nitrobenzoyl-CoA and extends it by 4 molecules of (S)-methylmalonyl-CoA and a single molecule of malonyl-CoA. The first module (encoded by aurA) is used twice in an iterative fashion, so that the five Claisen condensation reactions are catalysed by only four modules. The iteration becomes possible by the transfer of the [acp]-bound polyketide intermediate back to the ketosynthase (KS) domain on the opposite polyketide synthase strand (polyketides are homodimeric).
References:
1. He, J. and Hertweck, C. Iteration as programmed event during polyketide assembly; molecular analysis of the aureothin biosynthesis gene cluster. Chem. Biol. 10 (2003) 1225-1232. [PMID: 14700630]
2. He, J. and Hertweck, C. Functional analysis of the aureothin iterative type I polyketide synthase. Chembiochem 6 (2005) 908-912. [PMID: 15812854]
3. Busch, B., Ueberschaar, N., Sugimoto, Y. and Hertweck, C. Interchenar retrotransfer of aureothin intermediates in an iterative polyketide synthase module. J. Am. Chem. Soc. 134 (2012) 12382-12385. [PMID: 22799266]
Accepted name: spectinabilin polyketide synthase system
Reaction: 4-nitrobenzoyl-CoA + malonyl-CoA + 6 (S)-methylmalonyl-CoA + 6 NADPH + 4 H+ = demethyldeoxyspectinabilin + 7 CO2 + 8 CoA + 6 NADP+ + 5 H2O
For diagram of reaction, click here
Glossary: demethyldeoxyspectinabilin = 2-hydroxy-3,5-dimethyl-6-[(3E,5E,7E,9E)-3,5,7,9-tetramethyl-10-(4-nitrophenyl)deca-3,5,7,9-tetraen-1-yl]pyran-4-one
spectinabilin = 2-methoxy-3,5-dimethyl-6-[(2R,4Z)-4-[(2E,4E,6E)-2,4,6-trimethyl-7-(4-nitrophenyl)hepta-2,4,6-trien-1-ylidene]oxolan-2-yl]pyran-4-one
Other name(s): norAA’BC (gene names); spectinabilin polyketide synthase complex
Systematic name: malonyl-CoA/(S)-methylmalonyl-CoA:4-nitrobenzoyl-CoA (methyl)malonyltransferase (demethyldeoxyspectinabilin-forming)
Comments: This polyketide synthase, characterized from the bacteria Streptomyces orinoci and Streptomyces spectabilis, generates the backbone of the antibiotic spectinabilin. It is composed of 6 modules that total 28 domains and is encoded by four genes. The enzyme accepts the unusual starter unit 4-nitrobenzoyl-CoA and extends it by 6 molecules of (S)-methylmalonyl-CoA and a single molecule of malonyl-CoA. The first module (encoded by norA) is used twice in an iterative fashion, so that the seven Claisen condensation reactions are catalysed by only six modules. The iteration becomes possible by the transfer of the [acp]-bound polyketide intermediate back to the ketosynthase (KS) domain on the opposite polyketide synthase strand (polyketides are homodimeric).
References:
1. Traitcheva, N., Jenke-Kodama, H., He, J., Dittmann, E. and Hertweck, C. Non-colinear polyketide biosynthesis in the aureothin and neoaureothin pathways: an evolutionary perspective. Chembiochem 8 (2007) 1841-1849. [PMID: 17763486]
2. Choi, Y.S., Johannes, T.W., Simurdiak, M., Shao, Z., Lu, H. and Zhao, H. Cloning and heterologous expression of the spectinabilin biosynthetic gene cluster from Streptomyces spectabilis. Mol. Biosyst. 6 (2010) 336-338. [PMID: 20094652]
Accepted name: sphingoid base N-palmitoyltransferase
Reaction: palmitoyl-CoA + a sphingoid base = a C16 ceramide + CoA
Other name(s): mammalian ceramide synthase 5; CERS5 (gene name); LASS5 (gene name)
Systematic name: palmitoyl-CoA:sphingoid base N-palmitoyltransferase
Comments: Mammals have six ceramide synthases that exhibit relatively strict specificity regarding the chain-length of their acyl-CoA substrates. Ceramide synthase 5 (CERS5) is specific for palmitoyl-CoA as the acyl donor. It can use multiple sphingoid bases including sphinganine, sphingosine, and phytosphingosine.
References:
1. Lahiri, S. and Futerman, A.H. LASS5 is a bona fide dihydroceramide synthase that selectively utilizes palmitoyl-CoA as acyl donor. J. Biol. Chem 280 (2005) 33735-33738. [PMID: 16100120]
2. Xu, Z., Zhou, J., McCoy, D.M. and Mallampalli, R.K. LASS5 is the predominant ceramide synthase isoform involved in de novo sphingolipid synthesis in lung epithelia. J. Lipid Res. 46 (2005) 1229-1238. [PMID: 15772421]
3. Mizutani, Y., Kihara, A. and Igarashi, Y. Mammalian Lass6 and its related family members regulate synthesis of specific ceramides. Biochem. J. 390 (2005) 263-271. [PMID: 15823095]
Accepted name: 4-galactosyl-N-acetylglucosaminide 3-α-L-fucosyltransferase
Reaction: GDP-β-L-fucose + β-D-galactosyl-(1→4)-N-acetyl-D-glucosaminyl-R = GDP + β-D-galactosyl-(1→4)-[α-L-fucosyl-(1→3)]-N-acetyl-D-glucosaminyl-R
For diagram of reaction, click here
Other name(s): Lewis-negative α-3-fucosyltransferase; plasma α-3-fucosyltransferase; guanosine diphosphofucose-glucoside α1→3-fucosyltransferase; galactoside 3-fucosyltransferase; GDP-L-fucose:1,4-β-D-galactosyl-N-acetyl-D-glucosaminyl-R 3-L-fucosyltransferase; GDP-β-L-fucose:1,4-β-D-galactosyl-N-acetyl-D-glucosaminyl-R 3-L-fucosyltransferase; GDP-β-L-fucose:1,4-β-D-galactosyl-N-acetyl-D-glucosaminyl-R 3-α-L-fucosyltransferase; GDP-β-L-fucose:(1→4)-β-D-galactosyl-N-acetyl-D-glucosaminyl-R 3-α-L-fucosyltransferase
Systematic name: GDP-β-L-fucose:β-D-galactosyl-(1→4)-N-acetyl-D-glucosaminyl-R 3-α-L-fucosyltransferase
Comments: Normally acts on a glycoconjugate where R (see reaction) is a glycoprotein or glycolipid. This enzyme fucosylates on O-3 of an N-acetylglucosamine that carries a galactosyl group on O-4, unlike EC 2.4.1.65, 3-galactosyl-N-acetylglucosaminide 4-α-L-fucosyltransferase, which fucosylates on O-4 of an N-acetylglucosamine that carries a galactosyl group on O-3.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 39279-34-0
References:
1. Johnson, P.H., Yates, A.D. and Watkins, W.M. Human salivary fucosyltransferase: evidence for two distinct α-3-L-fucosyltransferase activities one of which is associated with the Lewis blood Le gene. Biochem. Biophys. Res. Commun. 100 (1981) 1611-1618. [PMID: 7295318]
2. Schachter, H., Narasimhan, S., Gleeson, P. and Vella, G. Glycosyltransferases involved in elongation of N-glycosidically linked oligosaccharides of the complex or N-acetyllactosamine type. Methods Enzymol. 98 (1983) 98-134. [PMID: 6366476]
3. Ma, B., Wang, G., Palcic, M.M., Hazes, B. and Taylor, D.E. C-terminal amino acids of Helicobacter pylori α1,3/4 fucosyltransferases determine type I and type II transfer. J. Biol. Chem. 278 (2003) 21893-21900. [PMID: 12676935]
Accepted name: enterobactin C-glucosyltransferase
Reaction: (1) UDP-α-D-glucose + enterobactin = UDP + monoglucosyl-enterobactin
(2) UDP-α-D-glucose + monoglucosyl-enterobactin = UDP + diglucosyl-enterobactin
(3) UDP-α-D-glucose + diglucosyl-enterobactin = UDP + triglucosyl-enterobactin
For diagram of reaction, click here
Glossary: enterobactin = N-(2,3-dihydroxybenzoyl)-O-[N-(2,3-dihydroxybenzoyl)-O-[N-(2,3-dihydroxybenzoyl)-L-seryl]-L-seryl]-L-serine-(3→1(3))-lactone
monoglucosyl-enterobactin = N-(2,3-dihydroxybenzoyl)-O-[N-(2,3-dihydroxybenzoyl)-O-[N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-L-seryl]-L-seryl]-L-serine-3→1(3)-lactone = mono-C-glucosyl-enterobactin = salmochelin MGE
diglucosyl-enterobactin = N-(2,3-dihydroxybenzoyl)-O-[N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-O-[N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-L-seryl]-L-seryl]-L-serine-(3→1(3))-lactone = salmochelin S4 = di-C-glucosyl-enterobactin
triglucosyl-enterobactin = N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-O-[N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-O-[N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-L-seryl]-L-seryl]-L-serine-(3→1(3))-lactone = tri-C-glucosyl-enterobactin = salmochelin TGE
Other name(s): iroB (gene name)
Systematic name: UDP-α-D-glucose:enterobactin 5'-C-β-D-glucosyltransferase (configuration-inverting)
Comments: The enzyme, found in pathogenic strains of the bacteria Escherichia coli and Salmonella enterica, catalyses the transfer of glucosyl groups to C-5 of one, two, or three of the 2,3-hydroxybenzoyl units of the siderophore enterobactin, forming C-glucosylated derivatives known as salmochelins.
References:
1. Fischbach, M.A., Lin, H., Liu, D.R. and Walsh, C.T. In vitro characterization of IroB, a pathogen-associated C-glycosyltransferase. Proc. Natl Acad. Sci. USA 102 (2005) 571-576. [PMID: 15598734]
Accepted name: inositol phosphorylceramide mannosyltransferase
Reaction: GDP-α-D-mannose + a very-long-chain inositol phospho-(2'R)-2'-hydroxyphytoceramide = a very-long-chain mannosylinositol phospho-(2'R)-2'-hydroxyphytoceramide + GDP
Glossary: a very-long-chain mannosylinositol phospho-(2'R)-2'-hydroxyphytoceramide = a very-long-chain mannosylinositol phospho-α-hydroxyphytoceramide = MIPC
Other name(s): SUR1 (gene name); CSH1 (gene name)
Systematic name: GDP-α-D-mannose:inositol phospho-(2'R)-2'-hydroxyphytoceramide mannosyltransferase
Comments: The simplest complex sphingolipid of yeast, inositol-phospho-α-hydroxyphytoceramide (IPC), is usually mannosylated to yield mannosyl-inositol-phospho-α hydroxyphytoceramide (MIPC). The enzyme is located in the Golgi apparatus, and utilizes GDP-mannose as the mannosyl group donor. It consists of a catalytic subunit (SUR1 or CSH1) and a regulatory subunit (CSG2).
References:
1. Beeler, T.J., Fu, D., Rivera, J., Monaghan, E., Gable, K. and Dunn, T.M. SUR1 (CSG1/BCL21), a gene necessary for growth of Saccharomyces cerevisiae in the presence of high Ca2+ concentrations at 37 degrees C, is required for mannosylation of inositolphosphorylceramide. Mol. Gen. Genet. 255 (1997) 570-579. [PMID: 9323360]
2. Dean, N., Zhang, Y.B. and Poster, J.B. The VRG4 gene is required for GDP-mannose transport into the lumen of the Golgi in the yeast, Saccharomyces cerevisiae. J. Biol. Chem 272 (1997) 31908-31914. [PMID: 9395539]
3. Uemura, S., Kihara, A., Inokuchi, J. and Igarashi, Y. Csg1p and newly identified Csh1p function in mannosylinositol phosphorylceramide synthesis by interacting with Csg2p. J. Biol. Chem 278 (2003) 45049-45055. [PMID: 12954640]
Accepted name: apo-salmochelin esterase
Reaction: (1) enterobactin + H2O = N-(2,3-dihydroxybenzoyl)-L-serine trimer
(2) triglucosyl-enterobactin + H2O = triglucosyl-(2,3-dihydroxybenzoylserine)3
(3) diglucosyl-enterobactin + H2O = diglucosyl-(2,3-dihydroxybenzoylserine)3
(4) monoglucosyl-enterobactin + H2O = monoglucosyl-(2,3-dihydroxybenzoylserine)3
For diagram of reaction, click here
Glossary: N-(2,3-dihydroxybenzoyl)-L-serine trimer = O-3-{O-3-[N-(2,3-dihydroxybenzoyl)-L-seryl]-N-(2,3-dihydroxybenzoyl)-L-seryl}-N-(2,3-dihydroxybenzoyl)-L-serine
diglucosyl-(2,3-dihydroxybenzoylserine)3 = salmochelin S2 = O-3-{O-3-[N-(2,3-dihydroxybenzoyl)-C-5-deoxy-β-D-glucosyl-L-seryl]-N-(2,3-dihydroxybenzoyl)-C-5-deoxy-β-D-glucosyl-L-seryl}-N-(2,3-dihydroxybenzoyl)-L-serine
enterobactin = N-(2,3-dihydroxybenzoyl)-O-[N-(2,3-dihydroxybenzoyl)-O-[N-(2,3-dihydroxybenzoyl)-L-seryl]-L-seryl]-L-serine-(3→1(3))-lactone
monoglucosyl-enterobactin = N-(2,3-dihydroxybenzoyl)-O-[N-(2,3-dihydroxybenzoyl)-O-[N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-L-seryl]-L-seryl]-L-serine-3→1(3)-lactone = mono-C-glucosyl-enterobactin = salmochelin MGE
diglucosyl-enterobactin = N-(2,3-dihydroxybenzoyl)-O-[N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-O-[N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-L-seryl]-L-seryl]-L-serine-(3→1(3))-lactone = salmochelin S4 = di-C-glucosyl-enterobactin
triglucosyl-enterobactin = N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-O-[N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-O-[N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-L-seryl]-L-seryl]-L-serine-(3→1(3))-lactone = tri-C-glucosyl-enterobactin = salmochelin TGE
Other name(s): iroE (gene name)
Systematic name: apo-salmochelin esterase
Comments: This bacterial enzyme is present in pathogenic Salmonella species, uropathogenic and avian pathogenic Escherichia coli strains, and certain Klebsiella strains. Unlike EC 3.1.1.108, ferric enterobactin esterase, which acts only on enterobactin, this enzyme can also act on the C-glucosylated forms known as salmochelins. Unlike EC 3.1.1.109, ferric salmochelin esterase (IroD), IroE prefers apo siderophores as substrates, and is assumed to act before the siderophores are exported out of the cell. It hydrolyses the trilactone only once, producing linearized trimers.
References:
1. Lin, H., Fischbach, M.A., Liu, D.R. and Walsh, C.T. In vitro characterization of salmochelin and enterobactin trilactone hydrolases IroD, IroE, and Fes. J. Am. Chem. Soc. 127 (2005) 11075-11084. [PMID: 16076215]
Accepted name: ferric enterobactin esterase
Reaction: iron(III)-enterobactin + 3 H2O = iron(III)-N-(2,3-dihydroxybenzoyl)-L-serine complex + 2 N-(2,3-dihydroxybenzoyl)-L-serine (overall reaction)
(1a) iron(III)-enterobactin + H2O = iron(III)-N-(2,3-dihydroxybenzoyl)-L-serine trimer complex
(1b) iron(III)-N-(2,3-dihydroxybenzoyl)-L-serine trimer complex + H2O = iron(III)-N-(2,3-dihydroxybenzoyl)-L-serine dimer complex + N-(2,3-dihydroxybenzoyl)-L-serine
(1c) iron(III)-N-(2,3-dihydroxybenzoyl)-L-serine dimer complex + H2O = iron(III)-N-(2,3-dihydroxybenzoyl)-L-serine complex + N-(2,3-dihydroxybenzoyl)-L-serine
Other name(s): fes (gene name); pfeE (gene name) enterochelin hydrolase; enterochelin esterase
Systematic name: iron(III)-enterobactin hydrolase
Comments: The enzyme, isolated from the bacterium Escherichia coli, allows the bacterium to grow in limited iron conditions. It can also act on enterobactin (with no complexed iron) and the aluminium(III) analogue of ferric enterobactin. The trimer formed is further hydrolysed to form the dimer and the monomer.
References:
1. O'Brien, I.G., Cox, G.B. and Gibson, F. Enterochelin hydrolysis and iron metabolism in Escherichia coli. Biochim. Biophys. Acta 237 (1971) 537-549. [PMID: 4330269]
2. Greenwood, K.T. and Luke, R.K. Enzymatic hydrolysis of enterochelin and its iron complex in Escherichia Coli K-12. Properties of enterochelin esterase. Biochim. Biophys. Acta 525 (1978) 209-218. [PMID: 150859]
3. Pettis, G.S. and McIntosh, M.A. Molecular characterization of the Escherichia coli enterobactin cistron entF and coupled expression of entF and the fes gene. J. Bacteriol. 169 (1987) 4154-4162. [PMID: 3040679]
4. Brickman, T.J. and McIntosh, M.A. Overexpression and purification of ferric enterobactin esterase from Escherichia coli. Demonstration of enzymatic hydrolysis of enterobactin and its iron complex. J. Biol. Chem 267 (1992) 12350-12355. [PMID: 1534808]
5. Winkelmann, G., Cansier, A., Beck, W. and Jung, G. HPLC separation of enterobactin and linear 2,3-dihydroxybenzoylserine derivatives: a study on mutants of Escherichia coli defective in regulation (fur), esterase (fes) and transport (fepA). Biometals 7 (1994) 149-154. [PMID: 8148617]
6. Perraud, Q., Moynie, L., Gasser, V., Munier, M., Godet, J., Hoegy, F., Mely, Y., Mislin, G.LA., Naismith, J.H. and Schalk, I.J. A key role for the periplasmic PfeE esterase in iron acquisition via the siderophore enterobactin in Pseudomonas aeruginosa. ACS Chem. Biol. 13 (2018) 2603-2614. [PMID: 30086222]
Accepted name: ferric salmochelin esterase
Reaction: (1) iron(III)-[diglucosyl-enterobactin] complex + H2O = iron(III)-[salmochelin S2] complex
(2) iron(III)-[monoglucosyl-enterobactin] complex + H2O = iron(III)-[monoglucosyl-(2,3-dihydroxybenzoylserine)3] complex
(3) iron(III)-[salmochelin S2] complex + H2O = iron(III)-[diglucosyl-(2,3-dihydroxybenzoylserine)2] complex + N-(2,3-dihydroxybenzoyl)-L-serine
(4) iron(III)-[salmochelin S2] complex + H2O = iron(III)-[salmochelin S1] complex + salmochelin SX
(5) iron(III)-[monoglucosyl-(2,3-dihydroxybenzoylserine)3] complex + H2O = iron(III)-[salmochelin S1] complex + N-(2,3-dihydroxybenzoyl)-L-serine
(6) iron(III)-[diglucosyl-(2,3-dihydroxybenzoylserine)2] complex + H2O = iron(III)-[salmochelin SX] complex + salmochelin SX
Glossary: salmochelin S2 = O-3-{O-3-[N-(2,3-dihydroxybenzoyl)-C-5-deoxy-β-D-glucosyl-L-seryl]-N-(2,3-dihydroxybenzoyl)-C-5-deoxy-β-D-glucosyl-L-seryl}-N-(2,3-dihydroxybenzoyl)-L-serine
salmochelin S1 = O-3-[N-(2,3-dihydroxybenzoyl)-L-seryl]-N-(C-5-deoxy-β-D-glucosyl-2,3-dihydroxybenzoyl)-L-serine
monoglucosyl-enterobactin = N-(2,3-dihydroxybenzoyl)-O-[N-(2,3-dihydroxybenzoyl)-O-[N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-L-seryl]-L-seryl]-L-serine-[3→1(3)]-lactone = mono-C-glucosyl-enterobactin = salmochelin MGE
diglucosyl-enterobactin = N-(2,3-dihydroxybenzoyl)-O-[N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-O-[N-(5-β-D-glucopyranosyl-2,3-dihydroxybenzoyl)-L-seryl]-L-seryl]-L-serine-[3→1(3)]-lactone = salmochelin S4 = di-C-glucosyl-enterobactin
salmochelin SX = N-(C-5-deoxy-β-D-glucosyl-2,3-dihydroxybenzoyl)-L-serine
Other name(s): iroD (gene name)
Systematic name: iron(III)-salmochelin complex hydrolase
Comments: This bacterial enzyme is present in pathogenic Salmonella species, uropathogenic and avian pathogenic Escherichia coli strains, and certain Klebsiella strains. The enzyme acts on iron(III)-bound enterobactin and C-glucosylated derivatives known as salmochelins. Unlike EC 3.1.1.107, apo-salmochelin esterase (IroE), IroD prefers iron(III)bound siderophores as substrates, and is assumed to act after the iron-siderophore complexes are imported into the cell. It catalyses several hydrolytic reactions, producing a mixture of iron(III)-[N-(2,3-dihydroxybenzoyl)-L-serine] complex and salmochelin SX.
References:
1. Lin, H., Fischbach, M.A., Liu, D.R. and Walsh, C.T. In vitro characterization of salmochelin and enterobactin trilactone hydrolases IroD, IroE, and Fes. J. Am. Chem. Soc. 127 (2005) 11075-11084. [PMID: 16076215]
Accepted name: 2-lysophosphatidate phosphatase
Reaction: a 1-acyl-sn-glycerol 3-phosphate + H2O = a 1-acyl-sn-glycerol + phosphate
Other name(s): 1-acyl-sn-glycerol 3-phosphatase; CPC3 (gene name); PHM8 (gene name)
Systematic name: 1-acyl-sn-glycerol 3-phosphate phosphohydrolase
Comments: The enzyme has been studied from the plants Arachis hypogaea (peanut) and Arabidopsis thaliana (thale cress) and from the yeast Saccharomyces cerevisiae. The enzyme from yeast, but not from the plants, requires Mg2+.
References:
1. Shekar, S., Tumaney, A.W., Rao, T.J. and Rajasekharan, R. Isolation of lysophosphatidic acid phosphatase from developing peanut cotyledons. Plant Physiol. 128 (2002) 988-996. [PMID: 11891254]
2. Reddy, V.S., Singh, A.K. and Rajasekharan, R. The Saccharomyces cerevisiae PHM8 gene encodes a soluble magnesium-dependent lysophosphatidic acid phosphatase. J. Biol. Chem 283 (2008) 8846-8854. [PMID: 18234677]
3. Reddy, V.S., Rao, D.K. and Rajasekharan, R. Functional characterization of lysophosphatidic acid phosphatase from Arabidopsis thaliana. Biochim. Biophys. Acta 1801 (2010) 455-461. [PMID: 20045079]
Accepted name: endoplasmic reticulum Man9GlcNAc2 1,2-α-mannosidase
Reaction: Man9GlcNAc2-[protein] + H2O = Man8GlcNAc2-[protein] (isomer 8A1,2,3B1,3) + D-mannopyranose
Glossary: Man9GlcNAc2-[protein] = {α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc}-N-Asn-[protein]
Man8GlcNAc2-[protein] (isomer 8A1,2,3B1,3) = {α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc}-N-Asn-[protein]
Other name(s): MAN1B1 (gene name); MNS1 (gene name); MNS3 (gene name)
Systematic name: Man9GlcNAc2-[protein]2-α-mannohydrolase (configuration-inverting)
Comments: The enzyme, located in the endoplasmic reticulum, primarily trims a single α-1,2-linked mannose residue from Man9GlcNAc2 to produce Man8GlcNAc2 isomer 8A1,2,3B1,3 (the names of the isomers listed here are based on a nomenclature system proposed by Prien et al [7]). The removal of the single mannosyl residue occurs in all eukaryotes as part of the processing of N-glycosylated proteins, and is absolutely essential for further elongation of the outer chain of properly-folded N-glycosylated proteins in yeast. In addition, the enzyme is involved in glycoprotein quality control at the ER quality control compartment (ERQC), helping to target misfolded glycoproteins for degradation. When present at very high concentrations in the ERQC, the enzyme can trim the carbohydrate chain further to Man(5-6)GlcNAc2.
References:
1. Jelinek-Kelly, S. and Herscovics, A. Glycoprotein biosynthesis in Saccharomyces cerevisiae. Purification of the α-mannosidase which removes one specific mannose residue from Man9GlcNAc. J. Biol. Chem. 263 (1988) 14757-14763. [PMID: 3049586]
2. Ziegler, F.D. and Trimble, R.B. Glycoprotein biosynthesis in yeast: purification and characterization of the endoplasmic reticulum Man9 processing α-mannosidase. Glycobiology 1 (1991) 605-614. [PMID: 1822240]
3. Gonzalez, D.S., Karaveg, K., Vandersall-Nairn, A.S., Lal, A. and Moremen, K.W. Identification, expression, and characterization of a cDNA encoding human endoplasmic reticulum mannosidase I, the enzyme that catalyzes the first mannose trimming step in mammalian Asn-linked oligosaccharide biosynthesis. J. Biol. Chem. 274 (1999) 21375-21386. [PMID: 10409699]
4. Herscovics, A., Romero, P.A. and Tremblay, L.O. The specificity of the yeast and human class I ER α 1,2-mannosidases involved in ER quality control is not as strict previously reported. Glycobiology 12 (2002) 14G-15G. [PMID: 12090241]
5. Avezov, E., Frenkel, Z., Ehrlich, M., Herscovics, A. and Lederkremer, G.Z. Endoplasmic reticulum (ER) mannosidase I is compartmentalized and required for N-glycan trimming to Man5-6GlcNAc2 in glycoprotein ER-associated degradation. Mol. Biol. Cell 19 (2008) 216-225. [PMID: 18003979]
6. Liebminger, E., Huttner, S., Vavra, U., Fischl, R., Schoberer, J., Grass, J., Blaukopf, C., Seifert, G.J., Altmann, F., Mach, L. and Strasser, R. Class I α-mannosidases are required for N-glycan processing and root development in Arabidopsis thaliana. Plant Cell 21 (2009) 3850-3867. [PMID: 20023195]
7. Prien, J.M., Ashline, D.J., Lapadula, A.J., Zhang, H. and Reinhold, V.N. The high mannose glycans from bovine ribonuclease B isomer characterization by ion trap MS. J. Am. Soc. Mass Spectrom. 20 (2009) 539-556. [PMID: 19181540]
Accepted name: Nα-acyl-L-glutamine aminoacylase
Reaction: an Nα-acyl-L-glutamine + H2O = L-glutamine + a carboxylate
Other name(s): agaA (gene name); axillary malodor releasing enzyme; AMRE
Systematic name: Nα-acyl-L-glutamine amidohydrolase (carboxylate-forming)
Comments: Requires Zn2+. The enzyme, characterized from the bacterium Corynebacterium sp. Ax20, hydrolyses odorless Nα-acyl-L-glutamine conjugates of short- and medium-chain fatty acids, releasing axillary malodor compounds. While the enzyme is highly specific for the L-glutamine moiety, it is quite promiscuous regarding the acyl moiety. The two most common products of the enzyme's activity in axillary secretions are (2E)-3-methylhex-2-enoate and 3-hydroxy-3-methylhexanoate.
References:
1. Natsch, A., Gfeller, H., Gygax, P., Schmid, J. and Acuna, G. A specific bacterial aminoacylase cleaves odorant precursors secreted in the human axilla. J. Biol. Chem. 278 (2003) 5718-5727. [PMID: 12468539]
2. Natsch, A., Gfeller, H., Gygax, P. and Schmid, J. Isolation of a bacterial enzyme releasing axillary malodor and its use as a screening target for novel deodorant formulations. Int J Cosmet Sci 27 (2005) 115-122. [PMID: 18492161]
3. Natsch, A., Derrer, S., Flachsmann, F. and Schmid, J. A broad diversity of volatile carboxylic acids, released by a bacterial aminoacylase from axilla secretions, as candidate molecules for the determination of human-body odor type. Chem. Biodivers. 3 (2006) 1-20. [PMID: 17193210]
Accepted name: valerianol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = valerianol + diphosphate
For diagram of reaction, click here
Glossary: valerianol = 2-[(2R,8R,8aS)-8,8a-dimethyl-1,2,3,4,6,7,8,8a-octahydronaphthalen-2-yl]propan-2-ol
Other name(s): ChTPS1 (gene name); CsiTPS8 (gene name)
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (valerianol-forming)
Comments: The enzyme was characterized from the trees Camellia hiemalis and Camellia sinensis (black tea). The enzyme from Camellia hiemalis produces (2Z,6E)-hedycaryol as a minor product.
References:
1. Hattan, J.I., Shindo, K., Sasaki, T., Ohno, F., Tokuda, H., Ishikawa, K. and Misawa, N. Identification of novel sesquiterpene synthase genes that mediate the biosynthesis of valerianol, which was an unknown ingredient of tea. Sci Rep 8 (2018) 12474. [PMID: 30127518]
Accepted name: D-ornithine—citrate ligase
Reaction: ATP + D-ornithine + citrate = AMP + diphosphate + N5-[(S)-citryl]-D-ornithine
For diagram of reaction, click here
Glossary: staphyloferrin A = N2-[(R)-citryl],N5-[(S)-citryl]-D-ornithine
Other name(s): sfnaD (gene name)
Systematic name: D-ornithine:citrate ligase {3-[(2-aminopentan-5-oylcarbamoyl)methyl]-3-hydroxybutanoate-forming}
Comments: Requires Mg2+. The enzyme, characterized from the bacterium Staphylococcus aureus, is involved in the biosynthesis of the siderophore staphyloferrin A. It belongs to a class of siderophore synthases known as type A nonribosomal peptide synthase-independent synthases (NIS). Type A NIS enzymes are responsible for the formation of amide or ester bonds between polyamines or amino alcohols and a prochiral carboxyl group of citrate. The enzyme forms a citrate adenylate intermediate prior to ligation.
References:
1. Cotton, J.L., Tao, J. and Balibar, C.J. Identification and characterization of the Staphylococcus aureus gene cluster coding for staphyloferrin A. Biochemistry 48 (2009) 1025-1035. [PMID: 19138128]
Accepted name: ABC-type Zn2+ transporter
Reaction: ATP + H2O + Zn2+-[zinc-binding protein][side 1] = ADP + phosphate + Zn2+[side 2] + [zinc-binding protein][side 1]
Other name(s): Zn2+-transporting ATPase; Zn2+ ABC transporter; znuABC (gene names)
Systematic name: ATP phosphohydrolase (ABC-type, Zn2+-importing)
Comments: ABC-type (ATP-binding cassette-type) transporter, characterized by the presence of two similar ATP-binding domains/proteins and two integral membrane domains/proteins. A bacterial enzyme that interacts with an extracytoplasmic substrate binding protein and mediates the high-affinity import of Zn2+.
References:
1. Patzer, S.I. and Hantke, K. The ZnuABC high-affinity zinc uptake system and its regulator Zur in Escherichia coli. Mol. Microbiol. 28 (1998) 1199-1210. [PMID: 9680209]
2. Hantke, K. Bacterial zinc uptake and regulators. Curr Opin Microbiol 8 (2005) 196-202. [PMID: 15802252]
Accepted name: ABC-type aliphatic sulfonate transporter
Reaction: ATP + H2O + aliphatic sulfonate-[sulfonate-binding protein][side 1] = ADP + phosphate + aliphatic sulfonate[side 2] + [sulfonate-binding protein][side 1]
Other name(s): aliphatic sulfonate transporting ATPase; alkane sulfonate ABC transporter; aliphatic sulfonate ABC transporter; ssuACB (gene names)
Systematic name: ATP phosphohydrolase (ABC-type, aliphatic sulfonate-importing)
Comments: ATP-binding cassette (ABC) type transporter, characterized by the presence of two similar ATP-binding domains/proteins and two integral membrane domains/proteins. The enzyme from the bacterium Escherichia coli K-12 interacts with an extracytoplasmic substrate binding protein and imports a broad range of aliphatic sulfonates for use as a source of sulfur.
References:
1. van Der Ploeg, J.R., Iwanicka-Nowicka, R., Bykowski, T., Hryniewicz, M.M. and Leisinger, T. The Escherichia coli ssuEADCB gene cluster is required for the utilization of sulfur from aliphatic sulfonates and is regulated by the transcriptional activator Cbl. J. Biol. Chem 274 (1999) 29358-29365. [PMID: 10506196]
2. Kertesz, M.A. Bacterial transporters for sulfate and organosulfur compounds. Res. Microbiol. 152 (2001) 279-290. [PMID: 11421275]
3. Davidson, A.L., Dassa, E., Orelle, C. and Chen, J. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72 (2008) 317. [PMID: 18535149]
Accepted name: ABC-type thiamine transporter
Reaction: ATP + H2O + thiamine-[thiamine-binding protein][side 1] = ADP + phosphate + thiamine[side 2] + [thiamine-binding protein][side 1]
Other name(s): thiamin transporting ATPase; thiamine ABC transporter; thiamin ABC transporter; thiamine transporting ATPase; thiBPQ (gene names)
Systematic name: ATP phosphohydrolase (ABC-type, thiamine-importing)
Comments: ATP-binding cassette (ABC) type transporter, characterized by the presence of two similar ATP-binding domains/proteins and two integral membrane domains/proteins. The enzyme, characterized from the bacterium Salmonella typhimurium, is a heterodimeric complex that interacts with an extracytoplasmic substrate binding protein and functions to import thiamine, thiamine monophosphate and thiamine diphosphate.
References:
1. Webb, E., Claas, K. and Downs, D. thiBPQ encodes an ABC transporter required for transport of thiamine and thiamine pyrophosphate in Salmonella typhimurium. J. Biol. Chem 273 (1998) 8946-8950. [PMID: 9535878]
Accepted name: ABC-type putrescine transporter
Reaction: ATP + H2O + putrescine-[putrescine-binding protein][side 1] = ADP + phosphate + putrescine[side 2] + [putrescine-binding protein][side 1]
Other name(s): putrescine transporting ATPase; putrescine ABC transporter; potFGHI (gene names)
Systematic name: ATP phosphohydrolase (ABC-type, putrescine-importing)
Comments: ATP-binding cassette (ABC) type transporter, characterized by the presence of two similar ATP-binding domains/proteins and two integral membrane domains/proteins. The enzyme from the bacterium Escherichia coli interacts with an extracytoplasmic substrate binding protein and mediates the high affinity uptake of putrescine. Differs in specificity from EC 7.6.2.11, ABC-type polyamine transporter.
References:
1. Pistocchi, R., Kashiwagi, K., Miyamoto, S., Nukui, E., Sadakata, Y., Kobayashi, H. and Igarashi, K. Characteristics of the operon for a putrescine transport system that maps at 19 minutes on the Escherichia coli chromosome. J. Biol. Chem 268 (1993) 146-152. [PMID: 8416922]
2. Terui, Y., Saroj, S.D., Sakamoto, A., Yoshida, T., Higashi, K., Kurihara, S., Suzuki, H., Toida, T., Kashiwagi, K. and Igarashi, K. Properties of putrescine uptake by PotFGHI and PuuP and their physiological significance in Escherichia coli. Amino Acids 46 (2014) 661-670. [PMID: 23719730]