The Enzyme Database

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EC 1.4.1.26     
Accepted name: 2,4-diaminopentanoate dehydrogenase (NAD+)
Reaction: (2R,4S)-2,4-diaminopentanoate + H2O + NAD+ = (2R)-2-amino-4-oxopentanoate + NH3 + NADH + H+
Other name(s): DAPDH (ambiguous)
Systematic name: (2R,4S)-2,4-diaminopentanoate:NADP+ oxidoreductase (deaminating)
Comments: The enzyme, characterized from an unknown bacterium in an environmental sample, has some activity with (2R,4R)-2,4-diaminopentanoate. It has very low activity with NADP+ (cf. EC 1.4.1.12, 2,4-diaminopentanoate dehydrogenase).
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc
References:
1.  Fonknechten, N., Perret, A., Perchat, N., Tricot, S., Lechaplais, C., Vallenet, D., Vergne, C., Zaparucha, A., Le Paslier, D., Weissenbach, J. and Salanoubat, M. A conserved gene cluster rules anaerobic oxidative degradation of L-ornithine. J. Bacteriol. 191 (2009) 3162–3167. [DOI] [PMID: 19251850]
[EC 1.4.1.26 created 2017]
 
 
EC 1.4.3.13     
Accepted name: protein-lysine 6-oxidase
Reaction: [protein]-L-lysine + O2 + H2O = [protein]-(S)-2-amino-6-oxohexanoate + NH3 + H2O2
Glossary: (S)-2-amino-6-oxohexanoate = L-allysine
Other name(s): lysyl oxidase
Systematic name: protein-L-lysine:oxygen 6-oxidoreductase (deaminating)
Comments: Also acts on protein 5-hydroxylysine. This enzyme catalyses the final known enzymic step required for collagen and elastin cross-linking in the biosynthesis of normal mature extracellular matrices [4]. These reactions play an important role for the development, elasticity and extensibility of connective tissue. The enzyme is also active on free amines, such as cadaverine or benzylamine [4,5]. Some isoforms can also use [protein]-N(6)-acetyl-L-lysine as substrate deacetamidating the substrate [6].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 99676-44-5
References:
1.  Harris, E.D., Gonnerman, W.A., Savage, J.E. and O'Dell, B.L. Connective tissue amine oxidase. II. Purification and partial characterization of lysyl oxidase from chick aorta. Biochim. Biophys. Acta 341 (1974) 332–344. [DOI] [PMID: 4838158]
2.  Rayton, J.K. and Harris, E.D. Induction of lysyl oxidase with copper. Properties of an in vitro system. J. Biol. Chem. 254 (1979) 621–626. [PMID: 33171]
3.  Stassen, F.L.H. Properties of highly purified lysyl oxidase from embryonic chick cartilage. Biochim. Biophys. Acta 438 (1976) 49–60. [DOI] [PMID: 7318]
4.  Palamakumbura, A.H. and Trackman, P.C. A fluorometric assay for detection of lysyl oxidase enzyme activity in biological samples. Anal. Biochem. 300 (2002) 245–251. [DOI] [PMID: 11779117]
5.  Kagan, H.M., Williams, M.A., Williamson, P.R. and Anderson, J.M. Influence of sequence and charge on the specificity of lysyl oxidase toward protein and synthetic peptide substrates. J. Biol. Chem. 259 (1984) 11203–11207. [PMID: 6147351]
6.  Rodriguez, H.M., Vaysberg, M., Mikels, A., McCauley, S., Velayo, A.C., Garcia, C. and Smith, V. Modulation of lysyl oxidase-like 2 enzymatic activity by an allosteric antibody inhibitor. J. Biol. Chem. 285 (2010) 20964–20974. [DOI] [PMID: 20439985]
7.  Kim, Y.M., Kim, E.C. and Kim, Y. The human lysyl oxidase-like 2 protein functions as an amine oxidase toward collagen and elastin. Mol. Biol. Rep. 38 (2011) 145–149. [DOI] [PMID: 20306300]
8.  Xu, L., Go, E.P., Finney, J., Moon, H., Lantz, M., Rebecchi, K., Desaire, H. and Mure, M. Post-translational modifications of recombinant human lysyl oxidase-like 2 (rhLOXL2) secreted from Drosophila S2 cells. J. Biol. Chem. 288 (2013) 5357–5363. [DOI] [PMID: 23319596]
9.  Ma, L., Huang, C., Wang, X.J., Xin, D.E., Wang, L.S., Zou, Q.C., Zhang, Y.S., Tan, M.D., Wang, Y.M., Zhao, T.C., Chatterjee, D., Altura, R.A., Wang, C., Xu, Y.S., Yang, J.H., Fan, Y.S., Han, B.H., Si, J., Zhang, X., Cheng, J., Chang, Z. and Chin, Y.E. Lysyl oxidase 3 is a dual-specificity enzyme involved in STAT3 deacetylation and deacetylimination modulation. Mol. Cell 65 (2017) 296–309. [PMID: 28065600]
[EC 1.4.3.13 created 1980, modified 1983]
 
 
EC 2.3.1.222     
Accepted name: phosphate propanoyltransferase
Reaction: propanoyl-CoA + phosphate = CoA + propanoyl phosphate
Other name(s): PduL
Systematic name: propanoyl-CoA:phosphate propanoyltransferase
Comments: Part of the degradation pathway for propane-1,2-diol .
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Liu, Y., Leal, N.A., Sampson, E.M., Johnson, C.L., Havemann, G.D. and Bobik, T.A. PduL is an evolutionarily distinct phosphotransacylase involved in B12-dependent 1,2-propanediol degradation by Salmonella enterica serovar typhimurium LT2. J. Bacteriol. 189 (2007) 1589–1596. [DOI] [PMID: 17158662]
[EC 2.3.1.222 created 2013]
 
 
EC 2.3.1.282     
Accepted name: phenolphthiocerol/phthiocerol/phthiodiolone dimycocerosyl transferase
Reaction: (1) 2 a mycocerosyl-[mycocerosic acid synthase] + a phthiocerol = a dimycocerosyl phthiocerol + 2 holo-[mycocerosic acid synthase]
(2) 2 a mycocerosyl-[mycocerosic acid synthase] + a phthiodiolone = a dimycocerosyl phthiodiolone + 2 holo-[mycocerosic acid synthase]
(3) 2 a mycocerosyl-[mycocerosic acid synthase] + a phenolphthiocerol = a dimycocerosyl phenolphthiocerol + 2 holo-[mycocerosic acid synthase]
Glossary: a mycocerosate = 2,4,6-trimethyl- and 2,4,6,8-tetramethyl-2-alkanoic acids present in many pathogenic mycobacteria. The chiral centers bearing the methyl groups have an L (levorotatory) stereo configuration.
a phthiocerol = a linear carbohydrate molecule to which one methoxyl group, one methyl group, and two secondary hydroxyl groups are attached.
a phthiodiolone = an intermediate in phthiocerol biosynthesis, containing an oxo group where phthiocerols contain a methoxyl group
a phenolphthiocerol = a compound related to phthiocerol that contains a phenol group at the ω end of the molecule
Other name(s): papA5 (gene name)
Systematic name: mycocerosyl-[mycocerosic acid synthase]:phenolphthiocerol/phthiocerol/phthiodiolone dimycocerosyl transferase
Comments: The enzyme, present in certain pathogenic species of mycobacteria, catalyses the transfer of mycocerosic acids to the two hydroxyl groups at the common lipid core of phthiocerol, phthiodiolone, and phenolphthiocerol, forming dimycocerosate esters. The fatty acid precursors of mycocerosic acids are activated by EC 6.2.1.49, long-chain fatty acid adenylyltransferase FadD28, which loads them onto EC 2.3.1.111, mycocerosate synthase. That enzyme extends the precursors to form mycocerosic acids that remain attached until transferred by EC 2.3.1.282.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Onwueme, K.C., Ferreras, J.A., Buglino, J., Lima, C.D. and Quadri, L.E. Mycobacterial polyketide-associated proteins are acyltransferases: proof of principle with Mycobacterium tuberculosis PapA5. Proc. Natl. Acad. Sci. USA 101 (2004) 4608–4613. [PMID: 15070765]
2.  Buglino, J., Onwueme, K.C., Ferreras, J.A., Quadri, L.E. and Lima, C.D. Crystal structure of PapA5, a phthiocerol dimycocerosyl transferase from Mycobacterium tuberculosis. J. Biol. Chem. 279 (2004) 30634–30642. [PMID: 15123643]
3.  Chavadi, S.S., Onwueme, K.C., Edupuganti, U.R., Jerome, J., Chatterjee, D., Soll, C.E. and Quadri, L.E. The mycobacterial acyltransferase PapA5 is required for biosynthesis of cell wall-associated phenolic glycolipids. Microbiology 158 (2012) 1379–1387. [PMID: 22361940]
4.  Touchette, M.H., Bommineni, G.R., Delle Bovi, R.J., Gadbery, J.E., Nicora, C.D., Shukla, A.K., Kyle, J.E., Metz, T.O., Martin, D.W., Sampson, N.S., Miller, W.T., Tonge, P.J. and Seeliger, J.C. Diacyltransferase activity and chain length specificity of Mycobacterium tuberculosis PapA5 in the synthesis of alkyl β-diol lipids. Biochemistry 54 (2015) 5457–5468. [DOI] [PMID: 26271001]
[EC 2.3.1.282 created 2019]
 
 
EC 2.7.1.195     
Accepted name: protein-Nπ-phosphohistidine—2-O-α-mannosyl-D-glycerate phosphotransferase
Reaction: [protein]-Nπ-phospho-L-histidine + 2-O-(α-D-mannopyranosyl)-D-glycerate [side 1] = [protein]-L-histidine + 2-O-(6-phospho-α-D-mannopyranosyl)-D-glycerate [side 2]
Other name(s): mngA (gene names); 2-O-α-mannosyl-D-glycerate PTS permease; EIIMngA; Enzyme IIMngA; Enzyme IIHrsA; EIImannosylglycerate; Frx
Systematic name: protein-Nπ-phospho-L-histidine:2-O-α-mannopyranosyl-D-glycerate Nπ-phosphotransferase
Comments: This enzyme is a component (known as enzyme II) of a phosphoenolpyruvate (PEP)-dependent, sugar transporting phosphotransferase system (PTS). The system, which is found only in prokaryotes, simultaneously transports its substrate from the periplasm or extracellular space into the cytoplasm and phosphorylates it. The phosphate donor, which is shared among the different systems, is a phospho-carrier protein of low molecular mass that has been phosphorylated by EC 2.7.3.9 (phosphoenolpyruvate—protein phosphotransferase). Enzyme II, on the other hand, is specific for a particular substrate, although in some cases alternative substrates can be transported with lower efficiency. The reaction involves a successive transfer of the phosphate group to several amino acids within the enzyme before the final transfer to the substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Sampaio, M.M., Chevance, F., Dippel, R., Eppler, T., Schlegel, A., Boos, W., Lu, Y.J. and Rock, C.O. Phosphotransferase-mediated transport of the osmolyte 2-O-α-mannosyl-D-glycerate in Escherichia coli occurs by the product of the mngA (hrsA) gene and is regulated by the mngR (farR) gene product acting as repressor. J. Biol. Chem. 279 (2004) 5537–5548. [DOI] [PMID: 14645248]
[EC 2.7.1.195 created 1972 as EC 2.7.1.69, part transferred 2016 to EC 2.7.1.195]
 
 
EC 2.7.7.100     
Accepted name: SAMP-activating enzyme
Reaction: ATP + [SAMP]-Gly-Gly = diphosphate + [SAMP]-Gly-Gly-AMP
Glossary: SAMP = small archaeal modifier protein = ubiquitin-like small archaeal modifier protein
Other name(s): UbaA (ambiguous); SAMP-activating enzyme E1 (ambiguous)
Systematic name: ATP:[SAMP]-Gly-Gly adenylyltransferase
Comments: Contains Zn2+. The enzyme catalyses the activation of SAMPs (Small Archaeal Modifier Proteins), which are ubiquitin-like proteins found only in the Archaea, by catalysing the ATP-dependent formation of a SAMP adenylate in which the C-terminal glycine of SAMP is bound to AMP via an acyl-phosphate linkage. The product of this activity can accept a sulfur atom to form a thiocarboxylate moiety that acts as a sulfur carrier involved in thiolation of tRNA and other metabolites such as molybdopterin. Alternatively, the enzyme can also catalyse the transfer of SAMP from its activated form to an internal cysteine residue, leading to a process termed SAMPylation (see EC 6.2.1.55, E1 SAMP-activating enzyme).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Miranda, H.V., Nembhard, N., Su, D., Hepowit, N., Krause, D.J., Pritz, J.R., Phillips, C., Soll, D. and Maupin-Furlow, J.A. E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea. Proc. Natl. Acad. Sci. USA 108 (2011) 4417–4422. [DOI] [PMID: 21368171]
2.  Maupin-Furlow, J.A. Ubiquitin-like proteins and their roles in archaea. Trends Microbiol. 21 (2013) 31–38. [DOI] [PMID: 23140889]
3.  Hepowit, N.L., de Vera, I.M., Cao, S., Fu, X., Wu, Y., Uthandi, S., Chavarria, N.E., Englert, M., Su, D., Söll, D., Kojetin, D.J. and Maupin-Furlow, J.A. Mechanistic insight into protein modification and sulfur mobilization activities of noncanonical E1 and associated ubiquitin-like proteins of Archaea. FEBS J. 283 (2016) 3567–3586. [DOI] [PMID: 27459543]
[EC 2.7.7.100 created 2018]
 
 
EC 3.2.1.177     
Accepted name: α-D-xyloside xylohydrolase
Reaction: Hydrolysis of terminal, non-reducing α-D-xylose residues with release of α-D-xylose.
Other name(s): α-xylosidase
Systematic name: α-D-xyloside xylohydrolase
Comments: The enzyme catalyses hydrolysis of a terminal, unsubstituted xyloside at the extreme reducing end of a xylogluco-oligosaccharide. Representative α-xylosidases from glycoside hydrolase family 31 utilize a two-step (double-displacement) mechanism involving a covalent glycosyl-enzyme intermediate, and retain the anomeric configuration of the product.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Moracci, M., Cobucci Ponzano, B., Trincone, A., Fusco, S., De Rosa, M., van Der Oost, J., Sensen, C.W., Charlebois, R.L. and Rossi, M. Identification and molecular characterization of the first α -xylosidase from an archaeon. J. Biol. Chem. 275 (2000) 22082–22089. [DOI] [PMID: 10801892]
2.  Sampedro, J., Sieiro, C., Revilla, G., Gonzalez-Villa, T. and Zarra, I. Cloning and expression pattern of a gene encoding an α-xylosidase active against xyloglucan oligosaccharides from Arabidopsis. Plant Physiol. 126 (2001) 910–920. [PMID: 11402218]
3.  Crombie, H.J., Chengappa, S., Jarman, C., Sidebottom, C. and Reid, J.S. Molecular characterisation of a xyloglucan oligosaccharide-acting α-D-xylosidase from nasturtium (Tropaeolum majus L.) cotyledons that resembles plant ’apoplastic’ α-D-glucosidases. Planta 214 (2002) 406–413. [PMID: 11859845]
4.  Lovering, A.L., Lee, S.S., Kim, Y.W., Withers, S.G. and Strynadka, N.C. Mechanistic and structural analysis of a family 31 α-glycosidase and its glycosyl-enzyme intermediate. J. Biol. Chem. 280 (2005) 2105–2115. [DOI] [PMID: 15501829]
5.  Iglesias, N., Abelenda, J.A., Rodino, M., Sampedro, J., Revilla, G. and Zarra, I. Apoplastic glycosidases active against xyloglucan oligosaccharides of Arabidopsis thaliana. Plant Cell Physiol. 47 (2006) 55–63. [DOI] [PMID: 16267099]
6.  Okuyama, M., Kaneko, A., Mori, H., Chiba, S. and Kimura, A. Structural elements to convert Escherichia coli α-xylosidase (YicI) into α-glucosidase. FEBS Lett. 580 (2006) 2707–2711. [DOI] [PMID: 16631751]
7.  Larsbrink, J., Izumi, A., Ibatullin, F., Nakhai, A., Gilbert, H.J., Davies, G.J. and Brumer, H. Structural and enzymatic characterisation of a glycoside hydrolase family 31 α-xylosidase from Cellvibrio japonicus involved in xyloglucan saccharification. Biochem. J. 436 (2011) 567–580. [DOI] [PMID: 21426303]
[EC 3.2.1.177 created 2011]
 
 
EC 3.4.19.15     
Accepted name: desampylase
Reaction: an N6-[small archaeal modifier protein]-[protein]-L-lysine + H2O = a [protein]-L-lysine + a small archaeal modifier protein
Glossary: SAMP = small archaeal modifier protein
Other name(s): SAMP-protein conjugate cleaving protease; HvJAMM1
Systematic name: N6-[small archaeal modifier protein]-[protein]-L-lysine hydrolase
Comments: The enzyme, characterized from the archaeon Haloferax volcanii, specifically cleaves the ubiquitin-like small modifier proteins SAMP1 and SAMP2 from protein conjugates, hydrolysing the isopeptide bond between a lysine residue of the target protein and the C-terminal glycine of the modifier protein. The enzyme contains Zn2+. cf. EC 3.4.19.12, ubiquitinyl hydrolase 1. In peptidase family M67.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hepowit, N.L., Uthandi, S., Miranda, H.V., Toniutti, M., Prunetti, L., Olivarez, O., De Vera, I.M., Fanucci, G.E., Chen, S. and Maupin-Furlow, J.A. Archaeal JAB1/MPN/MOV34 metalloenzyme (HvJAMM1) cleaves ubiquitin-like small archaeal modifier proteins (SAMPs) from protein-conjugates. Mol. Microbiol. 86 (2012) 971–987. [DOI] [PMID: 22970855]
[EC 3.4.19.15 created 2015 as EC 3.4.24.88, transferred 2016 to EC 3.4.19.15]
 
 
EC 3.4.24.88      
Transferred entry: desampylase. Transferred to EC 3.4.19.15 desampylase
[EC 3.4.24.88 created 2015, deleted 2016]
 
 
EC 4.2.2.1     
Accepted name: hyaluronate lyase
Reaction: Cleaves hyaluronate chains at a β-D-GlcNAc-(1→4)-β-D-GlcA bond, ultimately breaking the polysaccharide down to 3-(4-deoxy-β-D-gluc-4-enuronosyl)-N-acetyl-D-glucosamine.
Other name(s): hyaluronidase (ambiguous); glucuronoglycosaminoglycan lyase (ambiguous); spreading factor; mucinase (ambiguous)
Systematic name: hyaluronate lyase
Comments: The enzyme catalyses the degradation of hyaluronan by a β-elimination reaction. Also acts on chondroitin. The product is more systematically known as 3-(4-deoxy-α-L-threo-hex-4-enopyranosyluronic acid)-2-acetamido-2-deoxy-D-glucose
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37259-53-3
References:
1.  Linker, A., Hoffman, P., Meyer, K., Sampson, P. and Korn, E.D. The formation of unsaturated disacharides from mucopoly-saccharides and their cleavage to α-keto acid by bacterial enzymes. J. Biol. Chem. 235 (1960) 3061. [PMID: 13762462]
2.  Meyer, K. and Rapport, M.M. Hyaluronidases. Adv. Enzymol. Relat. Subj. Biochem. 13 (1952) 199–236. [PMID: 14943668]
3.  Moran, F., Nasuno, S. and Starr, M.P. Extracellular and intracellular polygalacturonic acid trans-eliminases of Erwinia carotovora. Arch. Biochem. Biophys. 123 (1968) 298–306. [DOI] [PMID: 5642600]
[EC 4.2.2.1 created 1961 as EC 4.2.99.1, transferred 1972 to EC 4.2.2.1, modified 2001]
 
 
EC 6.2.1.55     
Accepted name: E1 SAMP-activating enzyme
Reaction: ATP + [SAMP]-Gly-Gly + [E1 SAMP-activating enzyme]-L-cysteine = S-[[SAMP]-Gly-Gly]-[[E1 SAMP-activating enzyme]-L-cysteine] + AMP + diphosphate (overall reaction)
(1a) ATP + [SAMP]-Gly-Gly = diphosphate + [SAMP]-Gly-Gly-AMP
(1b) [SAMP]-Gly-Gly-AMP + [E1 SAMP-activating enzyme]-L-cysteine = S-[[SAMP]-Gly-Gly]-[[E1 SAMP-activating enzyme]-L-cysteine] + AMP
Glossary: SAMP = small archaeal modifier protein = ubiquitin-like small archaeal modifier protein
Other name(s): UbaA; SAMP-activating enzyme E1
Systematic name: [SAMP]:[E1 SAMP-activating enzyme] ligase (AMP-forming)
Comments: Contains Zn2+. The enzyme catalyses the activation of SAMPs (Small Archaeal Modifier Proteins), which are ubiquitin-like proteins found only in the Archaea. SAMPs are involved in protein degradation, and also act as sulfur carriers involved in thiolation of tRNA and other metabolites such as molybdopterin. The enzyme catalyses the ATP-dependent formation of a SAMP adenylate intermediate in which the C-terminal glycine of SAMP is bound to AMP via an acyl-phosphate linkage (reaction 1). This intermediate can accept a sulfur atom to form a thiocarboxylate moiety in a mechanism that is not yet understood. Alternatively, the E1 enzyme can transfer SAMP from its activated form to an internal cysteine residue, releasing AMP (reaction 2). In this case SAMP is subsequently transferred to a lysine residue in a target protein in a process termed SAMPylation. Auto-SAMPylation (attachment of SAMP to lysine residues within the E1 enzyme) has been observed. cf. EC 2.7.7.100, SAMP-activating enzyme.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Miranda, H.V., Nembhard, N., Su, D., Hepowit, N., Krause, D.J., Pritz, J.R., Phillips, C., Soll, D. and Maupin-Furlow, J.A. E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea. Proc. Natl. Acad. Sci. USA 108 (2011) 4417–4422. [DOI] [PMID: 21368171]
2.  Maupin-Furlow, J.A. Ubiquitin-like proteins and their roles in archaea. Trends Microbiol. 21 (2013) 31–38. [DOI] [PMID: 23140889]
3.  Miranda, H.V., Antelmann, H., Hepowit, N., Chavarria, N.E., Krause, D.J., Pritz, J.R., Basell, K., Becher, D., Humbard, M.A., Brocchieri, L. and Maupin-Furlow, J.A. Archaeal ubiquitin-like SAMP3 is isopeptide-linked to proteins via a UbaA-dependent mechanism. Mol. Cell. Proteomics 13 (2014) 220–239. [DOI] [PMID: 24097257]
4.  Hepowit, N.L., de Vera, I.M., Cao, S., Fu, X., Wu, Y., Uthandi, S., Chavarria, N.E., Englert, M., Su, D., Söll, D., Kojetin, D.J. and Maupin-Furlow, J.A. Mechanistic insight into protein modification and sulfur mobilization activities of noncanonical E1 and associated ubiquitin-like proteins of Archaea. FEBS J. 283 (2016) 3567–3586. [DOI] [PMID: 27459543]
[EC 6.2.1.55 created 2018]
 
 


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