The Enzyme Database

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EC 1.1.3.48     
Accepted name: 3-deoxy-α-D-manno-octulosonate 8-oxidase
Reaction: 3-deoxy-α-D-manno-octulopyranosonate + O2 = 3,8-dideoxy-8-oxo-α-D-manno-octulosonate + H2O2
Glossary: 3-deoxy-α-D-manno-octulosonate = Kdo
3,8-dideoxy-8-oxo-α-D-manno-octulosonate = (2R,4R,5R,6S)-2,4,5-trihydroxy-6-[(1S)-1-hydroxy-2-oxoethyl]oxane-2-carboxylate
Other name(s): kdnB (gene name)
Systematic name: 3-deoxy-α-D-manno-octulopyranosonate:oxygen 8-oxidoreductase
Comments: The enzyme, characterized from the bacterium Shewanella oneidensis, is involved in the formation of 8-amino-3,8-dideoxy-α-D-manno-octulosonate, an aminated form of Kdo found in lipopolysaccharides of members of the Shewanella genus. cf. EC 2.6.1.109, 8-amino-3,8-dideoxy-α-D-manno-octulosonate transaminase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Gattis, S.G., Chung, H.S., Trent, M.S. and Raetz, C.R. The origin of 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) in the lipopolysaccharide of Shewanella oneidensis. J. Biol. Chem. 288 (2013) 9216–9225. [DOI] [PMID: 23413030]
[EC 1.1.3.48 created 2015]
 
 
EC 1.3.1.14     
Accepted name: dihydroorotate dehydrogenase (NAD+)
Reaction: (S)-dihydroorotate + NAD+ = orotate + NADH + H+
Other name(s): orotate reductase (NADH); orotate reductase (NADH2); DHOdehase (ambiguous); DHOD (ambiguous); DHODase (ambiguous); dihydroorotate oxidase, pyrD (gene name)
Systematic name: (S)-dihydroorotate:NAD+ oxidoreductase
Comments: Binds FMN, FAD and a [2Fe-2S] cluster. The enzyme consists of two subunits, an FMN binding catalytic subunit and a FAD and iron-sulfur binding electron transfer subunit [4]. The reaction, which takes place in the cytosol, is the only redox reaction in the de-novo biosynthesis of pyrimidine nucleotides. Other class 1 dihydroorotate dehydrogenases use either fumarate (EC 1.3.98.1) or NADP+ (EC 1.3.1.15) as electron acceptor. The membrane bound class 2 dihydroorotate dehydrogenase (EC 1.3.5.2) uses quinone as electron acceptor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37255-26-8
References:
1.  Friedmann, H.C. and Vennesland, B. Purification and properties of dihydroorotic acid dehydrogenase. J. Biol. Chem. 233 (1958) 1398–1406. [PMID: 13610849]
2.  Friedmann, H.C. and Vennesland, B. Crystalline dihydroorotic dehydrogenase. J. Biol. Chem. 235 (1960) 1526–1532. [PMID: 13825167]
3.  Lieberman, I. and Kornberg, A. Enzymic synthesis and breakdown of a pyrimidine, orotic acid. I. Dihydro-orotic dehydrogenase. Biochim. Biophys. Acta 12 (1953) 223–234. [DOI] [PMID: 13115431]
4.  Nielsen, F.S., Andersen, P.S. and Jensen, K.F. The B form of dihydroorotate dehydrogenase from Lactococcus lactis consists of two different subunits, encoded by the pyrDb and pyrK genes, and contains FMN, FAD, and [FeS] redox centers. J. Biol. Chem. 271 (1996) 29359–29365. [DOI] [PMID: 8910599]
5.  Rowland, P., Nørager, S., Jensen, K.F. and Larsen, S. Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster. Structure 8 (2000) 1227–1238. [DOI] [PMID: 11188687]
6.  Kahler, A.E., Nielsen, F.S. and Switzer, R.L. Biochemical characterization of the heteromeric Bacillus subtilis dihydroorotate dehydrogenase and its isolated subunits. Arch. Biochem. Biophys. 371 (1999) 191–201. [DOI] [PMID: 10545205]
7.  Marcinkeviciene, J., Tinney, L.M., Wang, K.H., Rogers, M.J. and Copeland, R.A. Dihydroorotate dehydrogenase B of Enterococcus faecalis. Characterization and insights into chemical mechanism. Biochemistry 38 (1999) 13129–13137. [DOI] [PMID: 10529184]
[EC 1.3.1.14 created 1972, modified 2011]
 
 
EC 1.3.1.80      
Transferred entry: red chlorophyll catabolite reductase. Now classified as EC 1.3.7.12, red chlorophyll catabolite reductase
[EC 1.3.1.80 created 2007, deleted 2016]
 
 
EC 1.3.7.12     
Accepted name: red chlorophyll catabolite reductase
Reaction: primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster = red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
For diagram of chlorophyll catabolism, click here
Glossary: red chlorophyll catabolite = RCC = (7S,8S,101R)-8-(2-carboxyethyl)-17-ethyl-19-formyl-101-(methoxycarbonyl)-3,7,13,18-tetramethyl-2-vinyl-8,23-dihydro-7H-10,12-ethanobiladiene-ab-1,102(21H)-dione
primary fluorescent chlorophyll catabolite = pFCC = (82R,12S,13S)-12-(2-carboxyethyl)-3-ethyl-1-formyl-82-(methoxycarbonyl)-2,7,13,17-tetramethyl-18-vinyl-12,13-dihydro-8,10-ethanobilene-b-81,19(16H)-dione
Other name(s): RCCR; RCC reductase; red Chl catabolite reductase
Systematic name: primary fluorescent chlorophyll catabolite:ferredoxin oxidoreductase
Comments: The enzyme participates in chlorophyll degradation, which occurs during leaf senescence and fruit ripening in higher plants. The reaction requires reduced ferredoxin, which is generated from NADPH produced either through the pentose-phosphate pathway or by the action of photosystem I [1,2]. This reaction takes place while red chlorophyll catabolite is still bound to EC 1.14.15.17, pheophorbide a oxygenase [3]. Depending on the plant species used as the source of enzyme, one of two possible C-1 epimers of primary fluorescent chlorophyll catabolite (pFCC), pFCC-1 or pFCC-2, is normally formed, with all genera or species within a family producing the same isomer [3,4]. After modification and export, pFCCs are eventually imported into the vacuole, where the acidic environment causes their non-enzymic conversion into colourless breakdown products called non-fluorescent chlorophyll catabolites (NCCs) [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Rodoni, S., Mühlecker, W., Anderl, M., Kräutler, B., Moser, D., Thomas, H., Matile, P. and Hörtensteiner, S. Chlorophyll breakdown in senescent chloroplasts. Cleavage of pheophorbide a in two enzymic steps. Plant Physiol. 115 (1997) 669–676. [PMID: 12223835]
2.  Wüthrich, K.L., Bovet, L., Hunziker, P.E., Donnison, I.S. and Hörtensteiner, S. Molecular cloning, functional expression and characterisation of RCC reductase involved in chlorophyll catabolism. Plant J. 21 (2000) 189–198. [DOI] [PMID: 10743659]
3.  Pružinská, A., Anders, I., Aubry, S., Schenk, N., Tapernoux-Lüthi, E., Müller, T., Kräutler, B. and Hörtensteiner, S. In vivo participation of red chlorophyll catabolite reductase in chlorophyll breakdown. Plant Cell 19 (2007) 369–387. [DOI] [PMID: 17237353]
4.  Hörtensteiner, S. Chlorophyll degradation during senescence. Annu. Rev. Plant Biol. 57 (2006) 55–77. [DOI] [PMID: 16669755]
5.  Rodoni, S., Vicentini, F., Schellenberg, M., Matile, P. and Hörtensteiner, S. Partial purification and characterization of red chlorophyll catabolite reductase, a stroma protein involved in chlorophyll breakdown. Plant Physiol. 115 (1997) 677–682. [PMID: 12223836]
[EC 1.3.7.12 created 2007 as EC 1.3.1.80, transferred 2016 to EC 1.3.7.12]
 
 
EC 1.6.5.3      
Transferred entry: NADH:ubiquinone reductase (H+-translocating). Now EC 7.1.1.2, NADH:ubiquinone reductase (H+-translocating)
[EC 1.6.5.3 created 1961, deleted 1965, reinstated 1983, modified 2011, modified 2013, deleted 2018]
 
 
EC 1.8.4.2     
Accepted name: protein-disulfide reductase (glutathione)
Reaction: 2 glutathione + protein-disulfide = glutathione-disulfide + protein-dithiol
Other name(s): glutathione-insulin transhydrogenase; insulin reductase; reductase, protein disulfide (glutathione); protein disulfide transhydrogenase; glutathione-protein disulfide oxidoreductase; protein disulfide reductase (glutathione); GSH-insulin transhydrogenase; protein-disulfide interchange enzyme; protein-disulfide isomerase/oxidoreductase; thiol:protein-disulfide oxidoreductase; thiol-protein disulphide oxidoreductase
Systematic name: glutathione:protein-disulfide oxidoreductase
Comments: Reduces insulin and some other proteins.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9082-53-5
References:
1.  Katzen, H.M., Tietze, F. and Stetten, D. Further studies on the properties of hepatic glutathione-insulin transhydrogenase. J. Biol. Chem. 238 (1963) 1006–1011. [PMID: 14031343]
2.  Kohnert, K.-D., Hahn, H.-J., Zühlke, H., Schmidt, S. and Fiedler, H. Breakdown of exogenous insulin by Langerhans islets of the pancreas in vitro. Biochim. Biophys. Acta 338 (1974) 68–77.
[EC 1.8.4.2 created 1965]
 
 
EC 1.11.1.14     
Accepted name: lignin peroxidase
Reaction: (1) 1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol + H2O2 = 3,4-dimethoxybenzaldehyde + 2-methoxyphenol + glycolaldehyde + H2O
(2) 2 (3,4-dimethoxyphenyl)methanol + H2O2 = 2 (3,4-dimethoxyphenyl)methanol radical + 2 H2O
Glossary: veratryl alcohol = (3,4-dimethoxyphenyl)methanol
veratraldehyde = 3,4-dimethoxybenzaldehyde
2-methoxyphenol = guaiacol
Other name(s): diarylpropane oxygenase; ligninase I; diarylpropane peroxidase; LiP; diarylpropane:oxygen,hydrogen-peroxide oxidoreductase (C-C-bond-cleaving); 1,2-bis(3,4-dimethoxyphenyl)propane-1,3-diol:hydrogen-peroxide oxidoreductase (incorrect); (3,4-dimethoxyphenyl)methanol:hydrogen-peroxide oxidoreductase
Systematic name: 1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol:hydrogen-peroxide oxidoreductase
Comments: A hemoprotein, involved in the oxidative breakdown of lignin by white-rot basidiomycete fungi. The reaction involves an initial oxidation of the heme iron by hydrogen peroxide, forming compound I (FeIV=O radical cation) at the active site. A single one-electron reduction of compound I by an electron derived from a substrate molecule yields compound II (FeIV=O non-radical cation), followed by a second one-electron transfer that returns the enzyme to the ferric oxidation state. The electron transfer events convert the substrate molecule into a transient cation radical intermediate that fragments spontaneously. The enzyme can act on a wide range of aromatic compounds, including methoxybenzenes and nonphenolic β-O-4 linked arylglycerol β-aryl ethers, but cannot act directly on the lignin molecule, which is too large to fit into the active site. However larger lignin molecules can be degraded in the presence of veratryl alcohol. It has been suggested that the free radical that is formed when the enzyme acts on veratryl alcohol can diffuse into the lignified cell wall, where it oxidizes lignin and other organic substrates. In the presence of high concentration of hydrogen peroxide and lack of substrate, the enzyme forms a catalytically inactive form (compound III). This form can be rescued by interaction with two molecules of the free radical products. In the case of veratryl alcohol, such an interaction yields two molecules of veratryl aldehyde.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 93792-13-3
References:
1.  Kersten, P.J., Tien, M., Kalyanaraman, B. and Kirk, T.K. The ligninase of Phanerochaete chrysosporium generates cation radicals from methoxybenzenes. J. Biol. Chem. 260 (1985) 2609–2612. [PMID: 2982828]
2.  Paszczynski, A., Huynh, V.-B. and Crawford, R. Comparison of ligninase-I and peroxidase-M2 from the white-rot fungus Phanerochaete chrysosporium. Arch. Biochem. Biophys. 244 (1986) 750–765. [DOI] [PMID: 3080953]
3.  Harvey, P.J., Schoemaker, H.E. and Palmer, J.M. Veratryl alcohol as a mediator and the role of radical cations in lignin biodegradation by Phanerochaete chrysosporium. FEBS Lett. 195 (1986) 242–246.
4.  Wariishi, H., Marquez, L., Dunford, H.B. and Gold, M.H. Lignin peroxidase compounds II and III. Spectral and kinetic characterization of reactions with peroxides. J. Biol. Chem. 265 (1990) 11137–11142. [PMID: 2162833]
5.  Cai, D.Y. and Tien, M. Characterization of the oxycomplex of lignin peroxidases from Phanerochaete chrysosporium: equilibrium and kinetics studies. Biochemistry 29 (1990) 2085–2091. [PMID: 2328240]
6.  Khindaria, A., Yamazaki, I. and Aust, S.D. Veratryl alcohol oxidation by lignin peroxidase. Biochemistry 34 (1995) 16860–16869. [PMID: 8527462]
7.  Khindaria, A., Yamazaki, I. and Aust, S.D. Stabilization of the veratryl alcohol cation radical by lignin peroxidase. Biochemistry 35 (1996) 6418–6424. [DOI] [PMID: 8639588]
8.  Khindaria, A., Nie, G. and Aust, S.D. Detection and characterization of the lignin peroxidase compound II-veratryl alcohol cation radical complex. Biochemistry 36 (1997) 14181–14185. [DOI] [PMID: 9369491]
9.  Doyle, W.A., Blodig, W., Veitch, N.C., Piontek, K. and Smith, A.T. Two substrate interaction sites in lignin peroxidase revealed by site-directed mutagenesis. Biochemistry 37 (1998) 15097–15105. [DOI] [PMID: 9790672]
10.  Pollegioni, L., Tonin, F. and Rosini, E. Lignin-degrading enzymes. FEBS J. 282 (2015) 1190–1213. [DOI] [PMID: 25649492]
[EC 1.11.1.14 created 1992, modified 2006, modified 2011, modified 2016]
 
 
EC 1.13.11.36     
Accepted name: chloridazon-catechol dioxygenase
Reaction: 5-amino-4-chloro-2-(2,3-dihydroxyphenyl)-3(2H)-pyridazinone + O2 = 5-amino-4-chloro-2-(2-hydroxymuconoyl)-3(2H)-pyridazinone
Other name(s): 5-amino-4-chloro-2-(2,3-dihydroxyphenyl)-3(2H)-pyridazinone 1,2-oxidoreductase (decyclizing)
Systematic name: 5-amino-4-chloro-2-(2,3-dihydroxyphenyl)-3(2H)-pyridazinone 1,2-oxidoreductase (ring-opening)
Comments: An iron protein, requiring additional Fe2+. Not identical with EC 1.13.11.1 (catechol 1,2-dioxygenase), EC 1.13.11.2 (catechol 2,3-dioxygenase) or EC 1.13.11.5 (homogentisate 1,2-dioxygenase). Involved in the breakdown of the herbicide chloridazon.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 82869-32-7
References:
1.  Müller, R, Haug, S., Eberspächer, J. and Lingens, F. Catechol-2,3-Dioxygenase aus Pyrazon-abbauenden Bakterien. Hoppe-Seyler's Z. Physiol. Chem. 358 (1977) 797–805. [PMID: 19349]
2.  Müller, R., Schmitt, S. and Lingens, F. A novel non-heme iron-containing dioxygenase. Chloridazon-catechol dioxygenase from Phenylobacterium immobilis DSM 1986. Eur. J. Biochem. 125 (1982) 579–584. [DOI] [PMID: 6811270]
[EC 1.13.11.36 created 1984]
 
 
EC 1.13.12.5     
Accepted name: Renilla-type luciferase
Reaction: coelenterazine h + O2 = excited coelenteramide h monoanion + CO2 (over-all reaction)
(1a) coelenterazine h + O2 = coelenterazine h dioxetanone
(1b) coelenterazine h dioxetanone = excited coelenteramide h monoanion + CO2
For diagram of reaction, click here
Glossary: coelenterazine h = Renilla luciferin = 2,8-dibenzyl-6-(4-hydroxyphenyl)imidazo[1,2-a]pyrazin-3(7H)-one
coelenteramide h = Renilla oxyluciferin = N-[3-benzyl-5-(4-hydroxyphenyl)pyrazin-2-yl]-2-phenylacetamide
Other name(s): Renilla-luciferin 2-monooxygenase; luciferase (Renilla luciferin); Renilla-luciferin:oxygen 2-oxidoreductase (decarboxylating)
Systematic name: coelenterazine h:oxygen 2-oxidoreductase (decarboxylating)
Comments: This enzyme has been studied from the soft coral Renilla reniformis. Before the reaction occurs the substrate is sequestered by a coelenterazine-binding protein. Elevation in the concentration of calcium ions releases the substrate, which then interacts with the luciferase. Upon binding the substrate, the enzyme catalyses an oxygenation, producing a very short-lived hydroperoxide that cyclizes into a dioxetanone structure, which collapses, releasing a CO2 molecule. The spontaneous breakdown of the dioxetanone releases the energy (about 50 kcal/mole) that is necessary to generate the excited state of the coelenteramide product, which is the singlet form of the monoanion. In vivo the product undergoes the process of nonradiative energy transfer to an accessory protein, a green fluorescent protein (GFP), which results in green bioluminescence. In vitro, in the absence of GFP, the product emits blue light.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 61869-41-8
References:
1.  Cormier, M.J., Hori, K. and Anderson, J.M. Bioluminescence in coelenterates. Biochim. Biophys. Acta 346 (1974) 137–164. [PMID: 4154104]
2.  Hori, K., Anderson, J.M., Ward, W.W. and Cormier, M.J. Renilla luciferin as the substrate for calcium induced photoprotein bioluminescence. Assignment of luciferin tautomers in aequorin and mnemiopsin. Biochemistry 14 (1975) 2371–2376. [PMID: 237531]
3.  Anderson, J.M., Charbonneau, H. and Cormier, M.J. Mechanism of calcium induction of Renilla bioluminescence. Involvement of a calcium-triggered luciferin binding protein. Biochemistry 13 (1974) 1195–1200. [PMID: 4149963]
4.  Shimomura, O. and Johnson, F.H. Chemical nature of bioluminescence systems in coelenterates. Proc. Natl. Acad. Sci. USA 72 (1975) 1546–1549. [DOI] [PMID: 236561]
5.  Charbonneau, H. and Cormier, M.J. Ca2+-induced bioluminescence in Renilla reniformis. Purification and characterization of a calcium-triggered luciferin-binding protein. J. Biol. Chem. 254 (1979) 769–780. [PMID: 33174]
6.  Lorenz, W.W., McCann, R.O., Longiaru, M. and Cormier, M.J. Isolation and expression of a cDNA encoding Renilla reniformis luciferase. Proc. Natl. Acad. Sci. USA 88 (1991) 4438–4442. [DOI] [PMID: 1674607]
7.  Loening, A.M., Fenn, T.D. and Gambhir, S.S. Crystal structures of the luciferase and green fluorescent protein from Renilla reniformis. J. Mol. Biol. 374 (2007) 1017–1028. [DOI] [PMID: 17980388]
[EC 1.13.12.5 created 1976, modified 1981, modified 1982, modified 2004, modified 2017]
 
 
EC 1.13.12.7     
Accepted name: firefly luciferase
Reaction: D-firefly luciferin + O2 + ATP = firefly oxyluciferin + CO2 + AMP + diphosphate +
For diagram of reaction, click here
Glossary: D-firefly luciferin = Photinus-luciferin = (S)-4,5-dihydro-2-(6-hydroxy-1,3-benzothiazol-2-yl)thiazole-4-carboxylate
firefly oxyluciferin = 4,5-dihydro-2-(6-hydroxy-1,3-benzothiazol-2-yl)thiazol-4-one
Other name(s): Photinus-luciferin 4-monooxygenase (ATP-hydrolysing); luciferase (firefly luciferin); Photinus luciferin 4-monooxygenase (adenosine triphosphate-hydrolyzing); firefly luciferin luciferase; Photinus pyralis luciferase; Photinus-luciferin:oxygen 4-oxidoreductase (decarboxylating, ATP-hydrolysing)
Systematic name: D-firefly luciferin:oxygen 4-oxidoreductase (decarboxylating, ATP-hydrolysing)
Comments: The enzyme, which is found in fireflies (Lampyridae), is responsible for their biolouminescence. The reaction begins with the formation of an acid anhydride between the carboxylic group of D-firefly luciferin and AMP, with the release of diphosphate. An oxygenation follows, with release of the AMP group and formation of a very short-lived peroxide that cyclizes into a dioxetanone structure, which collapses, releasing a CO2 molecule. The spontaneous breakdown of the dioxetanone (rather than the hydrolysis of the adenylate) releases the energy (about 50 kcal/mole) that is necessary to generate the excited state of oxyluciferin. The excited luciferin then emits a photon, returning to its ground state. The enzyme has a secondary acyl-CoA ligase activity when acting on L-firefly luciferin (see EC 6.2.1.52).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 61970-00-1
References:
1.  Green, A. A. and McElroy, W. D. Crystalline firefly luciferase. Biochim. Biophys. Acta 20 (1956) 170–176. [DOI] [PMID: 13315363]
2.  White, E.H., McCapra, F., Field, G.F. and McElroy, W.D. The structure and synthesis of firefly luciferin. J. Am. Chem. Soc. 83 (1961) 2402–2403.
3.  Hopkins, T.A., Seliger, H.H., White, E.H. and Cass, M.W. The chemiluminescence of firefly luciferin. A model for the bioluminescent reaction and identification of the product excited state. J. Am. Chem. Soc. 89 (1967) 7148–7150. [PMID: 6064360]
4.  White, E.H., Rapaport, E., Hopkins, T.A. and Seliger, H.H. Chemi- and bioluminescence of firefly luciferin. J. Am. Chem. Soc. 91 (1969) 2178–2180. [PMID: 5784183]
5.  Koo, J.A., Schmidt, S.P. and Schuster, G.B. Bioluminescence of the firefly: key steps in the formation of the electronically excited state for model systems. Proc. Natl. Acad. Sci. USA 75 (1978) 30–33. [DOI] [PMID: 272645]
6.  de Wet, J.R., Wood, K.V., Helinski, D.R. and DeLuca, M. Cloning of firefly luciferase cDNA and the expression of active luciferase in Escherichia coli. Proc. Natl. Acad. Sci. USA 82 (1985) 7870–7873. [DOI] [PMID: 3906652]
7.  Nakamura, M., Maki, S., Amano, Y., Ohkita, Y., Niwa, K., Hirano, T., Ohmiya, Y. and Niwa, H. Firefly luciferase exhibits bimodal action depending on the luciferin chirality. Biochem. Biophys. Res. Commun. 331 (2005) 471–475. [DOI] [PMID: 15850783]
8.  Sundlov, J.A., Fontaine, D.M., Southworth, T.L., Branchini, B.R. and Gulick, A.M. Crystal structure of firefly luciferase in a second catalytic conformation supports a domain alternation mechanism. Biochemistry 51 (2012) 6493–6495. [DOI] [PMID: 22852753]
[EC 1.13.12.7 created 1976, modified 1981, modified 1982, modified 2017]
 
 
EC 1.14.12.20      
Transferred entry: pheophorbide a oxygenase. Now classified as EC 1.14.15.17, pheophorbide a oxygenase.
[EC 1.14.12.20 created 2007, deleted 2016]
 
 
EC 1.14.13.231     
Accepted name: tetracycline 11a-monooxygenase
Reaction: tetracycline + NADPH + H+ + O2 = 11a-hydroxytetracycline + NADP+ + H2O
For diagram of tetracycline biosynthesis, click here
Other name(s): tetX (gene name)
Systematic name: tetracycline,NADPH:oxygen oxidoreductase (11a-hydroxylating)
Comments: A flavoprotein (FAD). This bacterial enzyme confers resistance to all clinically relevant tetracyclines when expressed under aerobic conditions. The hydroxylated products are very unstable and lead to intramolecular cyclization and non-enzymic breakdown to undefined products.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yang, W., Moore, I.F., Koteva, K.P., Bareich, D.C., Hughes, D.W. and Wright, G.D. TetX is a flavin-dependent monooxygenase conferring resistance to tetracycline antibiotics. J. Biol. Chem. 279 (2004) 52346–52352. [DOI] [PMID: 15452119]
2.  Moore, I.F., Hughes, D.W. and Wright, G.D. Tigecycline is modified by the flavin-dependent monooxygenase TetX. Biochemistry 44 (2005) 11829–11835. [DOI] [PMID: 16128584]
3.  Volkers, G., Palm, G.J., Weiss, M.S., Wright, G.D. and Hinrichs, W. Structural basis for a new tetracycline resistance mechanism relying on the TetX monooxygenase. FEBS Lett. 585 (2011) 1061–1066. [DOI] [PMID: 21402075]
[EC 1.14.13.231 created 2016]
 
 
EC 1.14.15.17     
Accepted name: pheophorbide a oxygenase
Reaction: pheophorbide a + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2 = red chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster (overall reaction)
(1a) pheophorbide a + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2 = epoxypheophorbide a + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
(1b) epoxypheophorbide a + H2O = red chlorophyll catabolite (spontaneous)
For diagram of chlorophyll catabolism, click here
Glossary: red chlorophyll catabolite = RCC = (7S,8S,101R)-8-(2-carboxyethyl)-8,23-dihydro-17-ethyl-19-formyl-101-(methoxycarbonyl)-3,7,13,18-tetramethyl-2-vinyl-7H-10,12-ethanobiladiene-ab-1,102(21H)-dione
Other name(s): pheide a monooxygenase; pheide a oxygenase; PaO; PAO
Systematic name: pheophorbide-a,ferredoxin:oxygen oxidoreductase (biladiene-forming)
Comments: This enzyme catalyses a key reaction in chlorophyll degradation, which occurs during leaf senescence and fruit ripening in higher plants. The enzyme from Arabidopsis contains a Rieske-type iron-sulfur cluster [2] and requires reduced ferredoxin, which is generated either by NADPH through the pentose-phosphate pathway or by the action of photosystem I [4]. While still attached to this enzyme, the product is rapidly converted into primary fluorescent chlorophyll catabolite by the action of EC 1.3.7.12, red chlorophyll catabolite reductase [2,6]. Pheophorbide b acts as an inhibitor. In 18O2 labelling experiments, only the aldehyde oxygen is labelled, suggesting that the other oxygen atom may originate from H2O [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hörtensteiner, S., Wüthrich, K.L., Matile, P., Ongania, K.H. and Kräutler, B. The key step in chlorophyll breakdown in higher plants. Cleavage of pheophorbide a macrocycle by a monooxygenase. J. Biol. Chem. 273 (1998) 15335–15339. [DOI] [PMID: 9624113]
2.  Pružinská, A., Tanner, G., Anders, I., Roca, M. and Hörtensteiner, S. Chlorophyll breakdown: pheophorbide a oxygenase is a Rieske-type iron-sulfur protein, encoded by the accelerated cell death 1 gene. Proc. Natl. Acad. Sci. USA 100 (2003) 15259–15264. [DOI] [PMID: 14657372]
3.  Chung, D.W., Pružinská, A., Hörtensteiner, S. and Ort, D.R. The role of pheophorbide a oxygenase expression and activity in the canola green seed problem. Plant Physiol. 142 (2006) 88–97. [DOI] [PMID: 16844830]
4.  Rodoni, S., Mühlecker, W., Anderl, M., Kräutler, B., Moser, D., Thomas, H., Matile, P. and Hörtensteiner, S. Chlorophyll breakdown in senescent chloroplasts. Cleavage of pheophorbide a in two enzymic steps. Plant Physiol. 115 (1997) 669–676. [PMID: 12223835]
5.  Hörtensteiner, S. Chlorophyll degradation during senescence. Annu. Rev. Plant Biol. 57 (2006) 55–77. [DOI] [PMID: 16669755]
6.  Pružinská, A., Anders, I., Aubry, S., Schenk, N., Tapernoux-Lüthi, E., Müller, T., Kräutler, B. and Hörtensteiner, S. In vivo participation of red chlorophyll catabolite reductase in chlorophyll breakdown. Plant Cell 19 (2007) 369–387. [DOI] [PMID: 17237353]
[EC 1.14.15.17 created 2007 as EC 1.14.12.20, transferred 2016 to EC 1.14.15.17]
 
 
EC 2.3.1.16     
Accepted name: acetyl-CoA C-acyltransferase
Reaction: acyl-CoA + acetyl-CoA = CoA + 3-oxoacyl-CoA (overall reaction)
(1a) [acetyl-CoA C-acyltransferase]-S-acyl-L-cysteine + acetyl-CoA = 3-oxoacyl-CoA + [acetyl-CoA C-acyltransferase]-L-cysteine
(1b) acyl-CoA + [acetyl-CoA C-acyltransferase]-L-cysteine = [acetyl-CoA C-acyltransferase]-S-acyl-L-cysteine + CoA
For diagram of aerobic phenylacetate catabolism, click here and for diagram of Benzoyl-CoA catabolism, click here
Other name(s): β-ketothiolase; 3-ketoacyl-CoA thiolase; KAT; β-ketoacyl coenzyme A thiolase; β-ketoacyl-CoA thiolase; β-ketoadipyl coenzyme A thiolase; β-ketoadipyl-CoA thiolase; 3-ketoacyl CoA thiolase; 3-ketoacyl coenzyme A thiolase; 3-ketoacyl thiolase; 3-ketothiolase; 3-oxoacyl-CoA thiolase; 3-oxoacyl-coenzyme A thiolase; 6-oxoacyl-CoA thiolase; acetoacetyl-CoA β-ketothiolase; acetyl-CoA acyltransferase; ketoacyl-CoA acyltransferase; ketoacyl-coenzyme A thiolase; long-chain 3-oxoacyl-CoA thiolase; oxoacyl-coenzyme A thiolase; pro-3-ketoacyl-CoA thiolase; thiolase I; type I thiolase; 2-methylacetoacetyl-CoA thiolase [misleading]
Systematic name: acyl-CoA:acetyl-CoA C-acyltransferase
Comments: The enzyme, found in both eukaryotes and in prokaryotes, is involved in degradation pathways such as fatty acid β-oxidation. The enzyme acts on 3-oxoacyl-CoAs to produce acetyl-CoA and an acyl-CoA shortened by two carbon atoms. The reaction starts with the acylation of a nucleophilic cysteine at the active site by a 3-oxoacyl-CoA, with the concomitant release of acetyl-CoA. In the second step the acyl group is transferred to CoA. Most enzymes have a broad substrate range for the 3-oxoacyl-CoA. cf. EC 2.3.1.9, acetyl-CoA C-acetyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 9029-97-4
References:
1.  Beinert, H., Bock, R.M., Goldman, D.S., Green, D.E., Mahler, H.R., Mii, S., Stansly, P.G. and Wakil, S.J. A synthesis of dl-cortisone acetate. J. Am. Chem. Soc. 75 (1953) 4111–4112.
2.  Goldman, D.S. Studies on the fatty acid oxidizing system of animal tissue. VII. The β-ketoacyl coenzyme A cleavage enzyme. J. Biol. Chem. 208 (1954) 345–357. [PMID: 13174544]
3.  Stern, J.R., Coon, M.J. and del Campillo, A. Enzymatic breakdown and synthesis of acetoacetate. Nature 171 (1953) 28–30. [PMID: 13025466]
[EC 2.3.1.16 created 1961, modified 2019]
 
 
EC 2.3.1.241     
Accepted name: Kdo2-lipid IVA lauroyltransferase
Reaction: a dodecanoyl-[acyl-carrier protein] + Kdo2-lipid IVA = dodecanoyl-Kdo2-lipid IVA + an [acyl-carrier protein]
For diagram of Kdo-Kdo-Lipid IVA metabolism, click here
Glossary: Kdo = 3-deoxy-D-manno-oct-2-ulopyranosylonic acid
lipid IVA = 2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
Kdo2-lipid IVA = α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA
dodecanoyl = lauroyl
dodecanoyl-Kdo2-lipid IVA = α-Kdo-(2→4)-α-Kdo-(2→6)-2-deoxy-2-[(3R)-3-(dodecanoyloxy)tetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
Other name(s): LpxL; htrB (gene name); dodecanoyl-[acyl-carrier protein]:α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA O-dodecanoyltransferase; lauroyl-[acyl-carrier protein]:Kdo2-lipid IVA O-lauroyltransferase; (Kdo)2-lipid IVA lauroyltransferase; α-Kdo-(2→4)-α-(2→6)-lipid IVA lauroyltransferase
Systematic name: dodecanoyl-[acyl-carrier protein]:Kdo2-lipid IVA O-dodecanoyltransferase
Comments: The enzyme, characterized from the bacterium Escherichia coli, is involved in the biosynthesis of the phosphorylated outer membrane glycolipid lipid A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Clementz, T., Bednarski, J.J. and Raetz, C.R. Function of the htrB high temperature requirement gene of Escherichia coli in the acylation of lipid A: HtrB catalyzed incorporation of laurate. J. Biol. Chem. 271 (1996) 12095–12102. [DOI] [PMID: 8662613]
2.  Six, D.A., Carty, S.M., Guan, Z. and Raetz, C.R. Purification and mutagenesis of LpxL, the lauroyltransferase of Escherichia coli lipid A biosynthesis. Biochemistry 47 (2008) 8623–8637. [DOI] [PMID: 18656959]
[EC 2.3.1.241 created 2014]
 
 
EC 2.3.1.242     
Accepted name: Kdo2-lipid IVA palmitoleoyltransferase
Reaction: a (9Z)-hexadec-9-enoyl-[acyl-carrier protein] + Kdo2-lipid IVA = (9Z)-hexadec-9-enoyl-Kdo2-lipid IVA + an [acyl-carrier protein]
For diagram of Kdo-Kdo-Lipid IVA metabolism, click here
Glossary: Kdo = 3-deoxy-D-manno-oct-2-ulopyranosylonic acid
lipid IVA = 2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
Kdo2-lipid IVA = α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA
(9Z)-hexadec-9-enoyl = palmitoleoyl
(9Z)-hexadec-9-enoyl-Kdo2-lipid IVA = α-Kdo-(2→4)-α-Kdo-(2→6)-2-deoxy-2-{(3R)-3-[(9Z)-hexadec-9-enoyl]tetradecanamido}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
Other name(s): LpxP; palmitoleoyl-acyl carrier protein-dependent acyltransferase; cold-induced palmitoleoyl transferase; palmitoleoyl-[acyl-carrier protein]:Kdo2-lipid IVA O-palmitoleoyltransferase; (Kdo)2-lipid IVA palmitoleoyltransferase; α-Kdo-(2→4)-α-(2→6)-lipid IVA palmitoleoyltransferase
Systematic name: (9Z)-hexadec-9-enoyl-[acyl-carrier protein]:Kdo2-lipid IVA O-palmitoleoyltransferase
Comments: The enzyme, characterized from the bacterium Escherichia coli, is induced upon cold shock and is involved in the formation of a cold-adapted variant of the outer membrane glycolipid lipid A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Carty, S.M., Sreekumar, K.R. and Raetz, C.R. Effect of cold shock on lipid A biosynthesis in Escherichia coli. Induction At 12 degrees C of an acyltransferase specific for palmitoleoyl-acyl carrier protein. J. Biol. Chem. 274 (1999) 9677–9685. [DOI] [PMID: 10092655]
2.  Vorachek-Warren, M.K., Carty, S.M., Lin, S., Cotter, R.J. and Raetz, C.R. An Escherichia coli mutant lacking the cold shock-induced palmitoleoyltransferase of lipid A biosynthesis: absence of unsaturated acyl chains and antibiotic hypersensitivity at 12 degrees C. J. Biol. Chem. 277 (2002) 14186–14193. [DOI] [PMID: 11830594]
[EC 2.3.1.242 created 2014]
 
 
EC 2.3.1.243     
Accepted name: lauroyl-Kdo2-lipid IVA myristoyltransferase
Reaction: a tetradecanoyl-[acyl-carrier protein] + dodecanoyl-Kdo2-lipid IVA = dodecanoyl-(tetradecanoyl)-Kdo2-lipid IVA + an [acyl-carrier protein]
For diagram of Kdo-Kdo-Lipid IVA metabolism, click here
Glossary: Kdo = 3-deoxy-D-manno-oct-2-ulopyranosylonic acid
lipid IVA = 2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
Kdo2-lipid IVA = α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA
dodecanoyl = lauroyl
tetradecanoyl = myristoyl
dodecanoyl-Kdo2-lipid IVA = α-Kdo-(2→4)-α-Kdo-(2→6)-2-deoxy-2-[(3R)-3-(dodecanoyloxy)tetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
dodecanoyl-(tetradecanoyl)-Kdo2-lipid IVA = α-Kdo-(2→4)-α-Kdo-(2→6)-2-deoxy-2-[(3R)-3-(dodecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
Other name(s): MsbB acyltransferase; lpxM (gene name); myristoyl-[acyl-carrier protein]:α-Kdo-(2→4)-α-Kdo-(2→6)-(dodecanoyl)-lipid IVA O-myristoyltransferase
Systematic name: tetradecanoyl-[acyl-carrier protein]:dodecanoyl-Kdo2-lipid IVA O-tetradecanoyltransferase
Comments: The enzyme, characterized from the bacterium Escherichia coli, is involved in the biosynthesis of the phosphorylated outer membrane glycolipid lipid A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Clementz, T., Zhou, Z. and Raetz, C.R. Function of the Escherichia coli msbB gene, a multicopy suppressor of htrB knockouts, in the acylation of lipid A. Acylation by MsbB follows laurate incorporation by HtrB. J. Biol. Chem. 272 (1997) 10353–10360. [DOI] [PMID: 9099672]
[EC 2.3.1.243 created 2014]
 
 
EC 2.3.1.251     
Accepted name: lipid IVA palmitoyltransferase
Reaction: (1) 1-palmitoyl-2-acyl-sn-glycero-3-phosphocholine + hexa-acyl lipid A = 2-acyl-sn-glycero-3-phosphocholine + hepta-acyl lipid A
(2) 1-palmitoyl-2-acyl-sn-glycero-3-phosphocholine + lipid IIA = 2-acyl-sn-glycero-3-phosphocholine + lipid IIB
(3) 1-palmitoyl-2-acyl-sn-glycero-3-phosphocholine + lipid IVA = 2-acyl-sn-glycero-3-phosphocholine + lipid IVB
For diagram of lipid IVB biosynthesis, click here
Glossary: palmitoyl = hexadecanoyl
hexa-acyl lipid A = 2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
hepta-acyl lipid A = 2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-(hexadecanoyloxy)tetradecanamido]-α-D-glucopyranosyl phosphate
lipid IIA = 4-amino-4-deoxy-β-L-arabinopyranosyl 2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranose phosphate
lipid IIB = 4-amino-4-deoxy-β-L-arabinopyranosyl 2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-(hexadecanoyloxy)tetradecanamido]-α-D-glucopyranosyl phosphate
lipid IVA = 2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranose phosphate
lipid IVB = 2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-(hexadecanoyloxy)tetradecanamido]-α-D-glucopyranosyl phosphate
Other name(s): PagP; crcA (gene name)
Systematic name: 1-palmitoyl-2-acyl-sn-glycero-3-phosphocholine:lipid-IVA palmitoyltransferase
Comments: Isolated from the bacteria Escherichia coli and Salmonella typhimurium. The enzyme prefers phosphatidylcholine with a palmitoyl group at the sn-1 position and palmitoyl or stearoyl groups at the sn-2 position. There is some activity with corresponding phosphatidylserines but only weak activity with other diacylphosphatidyl compounds. The enzyme also acts on Kdo-(2→4)-Kdo-(2→6)-lipid IVA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bishop, R.E., Gibbons, H.S., Guina, T., Trent, M.S., Miller, S.I. and Raetz, C.R. Transfer of palmitate from phospholipids to lipid A in outer membranes of gram-negative bacteria. EMBO J. 19 (2000) 5071–5080. [DOI] [PMID: 11013210]
2.  Cuesta-Seijo, J.A., Neale, C., Khan, M.A., Moktar, J., Tran, C.D., Bishop, R.E., Pomes, R. and Prive, G.G. PagP crystallized from SDS/cosolvent reveals the route for phospholipid access to the hydrocarbon ruler. Structure 18 (2010) 1210–1219. [DOI] [PMID: 20826347]
[EC 2.3.1.251 created 2015]
 
 
EC 2.3.1.256     
Accepted name: N-terminal methionine Nα-acetyltransferase NatC
Reaction: (1) acetyl-CoA + an N-terminal-L-methionyl-L-leucyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-leucyl-[protein] + CoA
(2) acetyl-CoA + an N-terminal-L-methionyl-L-isoleucyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-isoleucyl-[protein] + CoA
(3) acetyl-CoA + an N-terminal-L-methionyl-L-phenylalanyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-phenylalanyl-[protein] + CoA
(4) acetyl-CoA + an N-terminal-L-methionyl-L-tryptophyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-tryptophyl-[protein] + CoA
(5) acetyl-CoA + an N-terminal-L-methionyl-L-tyrosyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-tyrosyl-[protein] + CoA
Other name(s): NAA30 (gene name); NAA35 (gene name); NAA38 (gene name); MAK3 (gene name); MAK10 (gene name); MAK31 (gene name)
Systematic name: acetyl-CoA:N-terminal-Met-Leu/Ile/Phe/Trp/Tyr-[protein] Met Nα-acetyltransferase
Comments: N-terminal-acetylases (NATs) catalyse the covalent attachment of an acetyl moiety from acetyl-CoA to the free α-amino group at the N-terminus of a protein. This irreversible modification neutralizes the positive charge at the N-terminus and makes the N-terminal residue larger and more hydrophobic, and may also play a role in membrane targeting and gene silencing. The NatC complex is found in all eukaryotic organisms, and specifically targets N-terminal L-methionine residues attached to bulky hydrophobic residues at the second position, including Leu, Ile, Phe, Trp, and Tyr residues.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Polevoda, B. and Sherman, F. NatC Nα-terminal acetyltransferase of yeast contains three subunits, Mak3p, Mak10p, and Mak31p. J. Biol. Chem. 276 (2001) 20154–20159. [DOI] [PMID: 11274203]
2.  Polevoda, B. and Sherman, F. Composition and function of the eukaryotic N-terminal acetyltransferase subunits. Biochem. Biophys. Res. Commun. 308 (2003) 1–11. [DOI] [PMID: 12890471]
3.  Pesaresi, P., Gardner, N.A., Masiero, S., Dietzmann, A., Eichacker, L., Wickner, R., Salamini, F. and Leister, D. Cytoplasmic N-terminal protein acetylation is required for efficient photosynthesis in Arabidopsis. Plant Cell 15 (2003) 1817–1832. [DOI] [PMID: 12897255]
4.  Wenzlau, J.M., Garl, P.J., Simpson, P., Stenmark, K.R., West, J., Artinger, K.B., Nemenoff, R.A. and Weiser-Evans, M.C. Embryonic growth-associated protein is one subunit of a novel N-terminal acetyltransferase complex essential for embryonic vascular development. Circ. Res. 98 (2006) 846–855. [DOI] [PMID: 16484612]
5.  Starheim, K.K., Gromyko, D., Evjenth, R., Ryningen, A., Varhaug, J.E., Lillehaug, J.R. and Arnesen, T. Knockdown of human Nα-terminal acetyltransferase complex C leads to p53-dependent apoptosis and aberrant human Arl8b localization. Mol. Cell Biol. 29 (2009) 3569–3581. [DOI] [PMID: 19398576]
[EC 2.3.1.256 created 1989 as EC 2.3.1.88, part transferred 2016 to EC 2.3.1.256]
 
 
EC 2.3.2.2     
Accepted name: γ-glutamyltransferase
Reaction: a (5-L-glutamyl)-peptide + an amino acid = a peptide + a 5-L-glutamyl amino acid
Other name(s): glutamyl transpeptidase; α-glutamyl transpeptidase; γ-glutamyl peptidyltransferase; γ-glutamyl transpeptidase (ambiguous); γ-GPT; γ-GT; γ-GTP; L-γ-glutamyl transpeptidase; L-γ-glutamyltransferase; L-glutamyltransferase; GGT (ambiguous); γ-glutamyltranspeptidase (ambiguous)
Systematic name: (5-L-glutamyl)-peptide:amino-acid 5-glutamyltransferase
Comments: The mammlian enzyme is part of the cell antioxidant defense mechanism. It initiates extracellular glutathione (GSH) breakdown, provides cells with a local cysteine supply and contributes to maintain intracelular GSH levels. The protein also has EC 3.4.19.13 (glutathione hydrolase) activity [3-4]. The enzyme consists of two chains that are created by the proteolytic cleavage of a single precursor polypeptide. The N-terminal L-threonine of the C-terminal subunit functions as the active site for both the cleavage and the hydrolysis reactions [3-4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9046-27-9
References:
1.  Goore, M.Y. and Thompson, J.F. γ-Glutamyl transpeptidase from kidney bean fruit. I. Purification and mechanism of action. Biochim. Biophys. Acta 132 (1967) 15–26. [DOI] [PMID: 6030345]
2.  Leibach, F.H. and Binkley, F. γ-Glutamyl transferase of swine kidney. Arch. Biochem. Biophys. 127 (1968) 292–301. [PMID: 5698023]
3.  Okada, T., Suzuki, H., Wada, K., Kumagai, H. and Fukuyama, K. Crystal structures of γ-glutamyltranspeptidase from Escherichia coli, a key enzyme in glutathione metabolism, and its reaction intermediate. Proc. Natl. Acad. Sci. USA 103 (2006) 6471–6476. [DOI] [PMID: 16618936]
4.  Boanca, G., Sand, A., Okada, T., Suzuki, H., Kumagai, H., Fukuyama, K. and Barycki, J.J. Autoprocessing of Helicobacter pylori γ-glutamyltranspeptidase leads to the formation of a threonine-threonine catalytic dyad. J. Biol. Chem. 282 (2007) 534–541. [DOI] [PMID: 17107958]
5.  Wickham, S., West, M.B., Cook, P.F. and Hanigan, M.H. Gamma-glutamyl compounds: substrate specificity of γ-glutamyl transpeptidase enzymes. Anal. Biochem. 414 (2011) 208–214. [DOI] [PMID: 21447318]
[EC 2.3.2.2 created 1972, modified 1976, modified 2011]
 
 
EC 2.4.1.1     
Accepted name: glycogen phosphorylase
Reaction: [(1→4)-α-D-glucosyl]n + phosphate = [(1→4)-α-D-glucosyl]n-1 + α-D-glucose 1-phosphate
For diagram of glycogen, click here
Other name(s): muscle phosphorylase a and b; amylophosphorylase; polyphosphorylase; amylopectin phosphorylase; glucan phosphorylase; α-glucan phosphorylase; 1,4-α-glucan phosphorylase; glucosan phosphorylase; granulose phosphorylase; maltodextrin phosphorylase; muscle phosphorylase; myophosphorylase; potato phosphorylase; starch phosphorylase; 1,4-α-D-glucan:phosphate α-D-glucosyltransferase; phosphorylase (ambiguous)
Systematic name: (1→4)-α-D-glucan:phosphate α-D-glucosyltransferase
Comments: This entry covers several enzymes from different sources that act in vivo on different forms of (1→4)-α-D-glucans. Some of these enzymes catalyse the first step in the degradation of large branched glycan polymers - the phosphorolytic cleavage of α-1,4-glucosidic bonds from the non-reducing ends of linear poly(1→4)-α-D-glucosyl chains within the polymers. The enzyme stops when it reaches the fourth residue away from an α-1,6 branching point, leaving a highly branched core known as a limit dextrin. The accepted name of the enzyme should be modified for each specific instance by substituting "glycogen" with the name of the natural substrate, e.g. maltodextrin phosphorylase, starch phosphorylase, etc.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9035-74-9
References:
1.  Hanes, C.S. The breakdown and synthesis of starch by an enzyme from pea seeds. Proc. R. Soc. Lond. B Biol. Sci. 128 (1940) 421–450.
2.  Green, A.A. and Cori, G.T. Crystalline muscle phosphorylase. I. Preparation, properties, and molecular weight. J. Biol. Chem. 151 (1943) 21–29.
3.  Baum, H. and Gilbert, G.A. A simple method for the preparation of crystalline potato phosphorylase and Q-enzyme. Nature 171 (1953) 983–984. [PMID: 13063502]
4.  Cowgill, R.W. Lobster muscle phosphorylase: purfication and properties. J. Biol. Chem. 234 (1959) 3146–3153. [PMID: 13812491]
5.  Chen, G.S. and Segel, I.H. Purification and properties of glycogen phosphorylase from Escherichia coli. Arch. Biochem. Biophys. 127 (1968) 175–186. [DOI] [PMID: 4878695]
6.  Fischer, E.H., Pocker, A. and Saari, J.C. The structure, function and control of glycogen phosphorylase. In: Campbell, P.N. and Greville, G.D. (Ed.), Essays in Biochemistry, vol. 6, Academic Press, London and New York, 1970, pp. 23–68.
[EC 2.4.1.1 created 1961, modified 2013]
 
 
EC 2.4.2.28     
Accepted name: S-methyl-5′-thioadenosine phosphorylase
Reaction: S-methyl-5′-thioadenosine + phosphate = adenine + S-methyl-5-thio-α-D-ribose 1-phosphate
For diagram of methionine salvage, click here
Other name(s): 5′-deoxy-5′-methylthioadenosine phosphorylase; MTA phosphorylase; MeSAdo phosphorylase; MeSAdo/Ado phosphorylase; methylthioadenosine phosphorylase; methylthioadenosine nucleoside phosphorylase; 5′-methylthioadenosine:phosphate methylthio-D-ribosyl-transferase; S-methyl-5-thioadenosine phosphorylase; S-methyl-5-thioadenosine:phosphate S-methyl-5-thio-α-D-ribosyl-transferase
Systematic name: S-methyl-5′-thioadenosine:phosphate S-methyl-5-thio-α-D-ribosyl-transferase
Comments: Also acts on 5′-deoxyadenosine and other analogues having 5′-deoxy groups.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 61970-06-7
References:
1.  Carteni-Farina, M., Oliva, A., Romeo, G., Napolitano, G., De Rosa, M., Gambacorta, A. and Zappia, V. 5′-Methylthioadenosine phosphorylase from Caldariella acidophila. Purification and properties. Eur. J. Biochem. 101 (1979) 317–324. [DOI] [PMID: 118001]
2.  Garbers, D.L. Demonstration of 5′-methylthioadenosine phosphorylase activity in various rat tissues. Some properties of the enzyme from rat lung. Biochim. Biophys. Acta 523 (1978) 82–93. [DOI] [PMID: 415762]
3.  Pegg, A.E. and Williams-Ashman, H.G. Phosphate-stimulated breakdown of 5′-methylthioadenosine by rat ventral prostate. Biochem. J. 115 (1969) 241–247. [PMID: 5378381]
[EC 2.4.2.28 created 1983]
 
 
EC 2.4.2.43     
Accepted name: lipid IVA 4-amino-4-deoxy-L-arabinosyltransferase
Reaction: (1) 4-amino-4-deoxy-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate + α-Kdo-(2→4)-α-Kdo-(2→6)-lipid A = α-Kdo-(2→4)-α-Kdo-(2→6)-[4-P-L-Ara4N]-lipid A + ditrans,octacis-undecaprenyl phosphate
(2) 4-amino-4-deoxy-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate + lipid IVA = lipid IIA + ditrans,octacis-undecaprenyl phosphate
(3) 4-amino-4-deoxy-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate + α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = 4′-α-L-Ara4N-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA + ditrans,octacis-undecaprenyl phosphate
For diagram of lipid IIA biosynthesis, click here
Glossary: lipid IVA = 2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
lipid IIA = 4-amino-4-deoxy-β-L-arabinopyranosyl 2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-α-D-glucopyranosyl phosphate
α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
4′-α-L-Ara4N-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = 4-amino-4-deoxy-α-L-arabinopyranosyl 2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-phospho-β-D-glucopyranosy-(1→6)-2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-α-D-glucopyranosyl phosphate
lipid A = lipid A of Escherichia coli = 2-deoxy-2-{[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino}-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
α-Kdo-(2→4)-α-Kdo-(2→6)-lipid A = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino}-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
α-Kdo-(2→4)-α-Kdo-(2→6)-[4′-P-α-L-Ara4N]-lipid A = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino}-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-(4-amino-4-deoxy-α-L-arabinopyranosyl)phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
Other name(s): undecaprenyl phosphate-α-L-Ara4N transferase; 4-amino-4-deoxy-L-arabinose lipid A transferase; polymyxin resistance protein PmrK; arnT (gene name)
Systematic name: 4-amino-4-deoxy-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate:lipid IVA 4-amino-4-deoxy-L-arabinopyranosyltransferase
Comments: Integral membrane protein present in the inner membrane of certain Gram negative endobacteria. In strains that do not produce 3-deoxy-D-manno-octulosonic acid (Kdo), the enzyme adds a single arabinose unit to the 1-phosphate moiety of the tetra-acylated lipid A precursor, lipid IVA. In the presence of a Kdo disaccharide, the enzyme primarily adds an arabinose unit to the 4-phosphate of lipid A molecules. The Salmonella typhimurium enzyme can add arabinose units to both positions.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Trent, M.S., Ribeiro, A.A., Lin, S., Cotter, R.J. and Raetz, C.R. An inner membrane enzyme in Salmonella and Escherichia coli that transfers 4-amino-4-deoxy-L-arabinose to lipid A: induction on polymyxin-resistant mutants and role of a novel lipid-linked donor. J. Biol. Chem. 276 (2001) 43122–43131. [DOI] [PMID: 11535604]
2.  Trent, M.S., Ribeiro, A.A., Doerrler, W.T., Lin, S., Cotter, R.J. and Raetz, C.R. Accumulation of a polyisoprene-linked amino sugar in polymyxin-resistant Salmonella typhimurium and Escherichia coli: structural characterization and transfer to lipid A in the periplasm. J. Biol. Chem. 276 (2001) 43132–43144. [DOI] [PMID: 11535605]
3.  Zhou, Z., Ribeiro, A.A., Lin, S., Cotter, R.J., Miller, S.I. and Raetz, C.R. Lipid A modifications in polymyxin-resistant Salmonella typhimurium: PMRA-dependent 4-amino-4-deoxy-L-arabinose, and phosphoethanolamine incorporation. J. Biol. Chem. 276 (2001) 43111–43121. [DOI] [PMID: 11535603]
4.  Bretscher, L.E., Morrell, M.T., Funk, A.L. and Klug, C.S. Purification and characterization of the L-Ara4N transferase protein ArnT from Salmonella typhimurium. Protein Expr. Purif. 46 (2006) 33–39. [DOI] [PMID: 16226890]
5.  Impellitteri, N.A., Merten, J.A., Bretscher, L.E. and Klug, C.S. Identification of a functionally important loop in Salmonella typhimurium ArnT. Biochemistry 49 (2010) 29–35. [DOI] [PMID: 19947657]
[EC 2.4.2.43 created 2010, modified 2011]
 
 
EC 2.4.99.12     
Accepted name: lipid IVA 3-deoxy-D-manno-octulosonic acid transferase
Reaction: lipid IVA + CMP-β-Kdo = α-Kdo-(2→6)-lipid IVA + CMP
For diagram of Kdo4-Lipid IVA biosynthesis, click here
Glossary: lipid IVA = 2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
(Kdo)-lipid IVA = α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
CMP-β-Kdo = CMP-3-deoxy-β-D-manno-oct-2-ulopyranosylonate
Other name(s): KDO transferase; waaA (gene name); kdtA (gene name); 3-deoxy-D-manno-oct-2-ulosonic acid transferase; 3-deoxy-manno-octulosonic acid transferase; lipid IVA KDO transferase
Systematic name: CMP-3-deoxy-D-manno-oct-2-ulosonate:lipid IVA 3-deoxy-D-manno-oct-2-ulosonate transferase
Comments: The bifunctional enzyme from Escherichia coli transfers two 3-deoxy-D-manno-oct-2-ulosonate residues to lipid IVA (cf. EC 2.4.99.13 [(Kdo)-lipid IVA 3-deoxy-D-manno-octulosonic acid transferase]) [1]. The monofunctional enzymes from Aquifex aeolicus and Haemophilus influenzae catalyse the transfer of a single 3-deoxy-D-manno-oct-2-ulosonate residue from CMP-3-deoxy-D-manno-oct-2-ulosonate to lipid IVA [2,3]. The enzymes from Chlamydia transfer three or more 3-deoxy-D-manno-oct-2-ulosonate residues and generate genus-specific epitopes [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Belunis, C.J. and Raetz, C.R. Biosynthesis of endotoxins. Purification and catalytic properties of 3-deoxy-D-manno-octulosonic acid transferase from Escherichia coli. J. Biol. Chem. 267 (1992) 9988–9997. [PMID: 1577828]
2.  Mamat, U., Schmidt, H., Munoz, E., Lindner, B., Fukase, K., Hanuszkiewicz, A., Wu, J., Meredith, T.C., Woodard, R.W., Hilgenfeld, R., Mesters, J.R. and Holst, O. WaaA of the hyperthermophilic bacterium Aquifex aeolicus is a monofunctional 3-deoxy-D-manno-oct-2-ulosonic acid transferase involved in lipopolysaccharide biosynthesis. J. Biol. Chem. 284 (2009) 22248–22262. [DOI] [PMID: 19546212]
3.  White, K.A., Kaltashov, I.A., Cotter, R.J. and Raetz, C.R. A mono-functional 3-deoxy-D-manno-octulosonic acid (Kdo) transferase and a Kdo kinase in extracts of Haemophilus influenzae. J. Biol. Chem. 272 (1997) 16555–16563. [DOI] [PMID: 9195966]
4.  Lobau, S., Mamat, U., Brabetz, W. and Brade, H. Molecular cloning, sequence analysis, and functional characterization of the lipopolysaccharide biosynthetic gene kdtA encoding 3-deoxy-α-D-manno-octulosonic acid transferase of Chlamydia pneumoniae strain TW-183. Mol. Microbiol. 18 (1995) 391–399. [DOI] [PMID: 8748024]
[EC 2.4.99.12 created 2010, modified 2011]
 
 
EC 2.4.99.13     
Accepted name: (Kdo)-lipid IVA 3-deoxy-D-manno-octulosonic acid transferase
Reaction: α-Kdo-(2→6)-lipid IVA + CMP-β-Kdo = α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA + CMP
For diagram of Kdo4-Lipid IVA biosynthesis, click here
Glossary: (Kdo)-lipid IVA = α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
(Kdo)2-lipid IVA = α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
CMP-β-Kdo = CMP-3-deoxy-β-D-manno-oct-2-ulopyranosylonate
Other name(s): Kdo transferase; waaA (gene name); kdtA (gene name); 3-deoxy-D-manno-oct-2-ulosonic acid transferase; 3-deoxy-manno-octulosonic acid transferase; (KDO)-lipid IVA 3-deoxy-D-manno-octulosonic acid transferase
Systematic name: CMP-3-deoxy-D-manno-oct-2-ulosonate:(Kdo)-lipid IVA 3-deoxy-D-manno-oct-2-ulosonate transferase
Comments: The bifunctional enzyme from Escherichia coli transfers two 3-deoxy-D-manno-oct-2-ulosonate residues to lipid IVA (cf. EC 2.4.99.12 [lipid IVA 3-deoxy-D-manno-octulosonic acid transferase]) [1]. The enzymes from Chlamydia transfer three or more 3-deoxy-D-manno-oct-2-ulosonate residues and generate genus-specific epitopes [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Belunis, C.J. and Raetz, C.R. Biosynthesis of endotoxins. Purification and catalytic properties of 3-deoxy-D-manno-octulosonic acid transferase from Escherichia coli. J. Biol. Chem. 267 (1992) 9988–9997. [PMID: 1577828]
2.  Lobau, S., Mamat, U., Brabetz, W. and Brade, H. Molecular cloning, sequence analysis, and functional characterization of the lipopolysaccharide biosynthetic gene kdtA encoding 3-deoxy-α-D-manno-octulosonic acid transferase of Chlamydia pneumoniae strain TW-183. Mol. Microbiol. 18 (1995) 391–399. [DOI] [PMID: 8748024]
[EC 2.4.99.13 created 2010, modified 2011]
 
 
EC 2.4.99.14     
Accepted name: (Kdo)2-lipid IVA (2-8) 3-deoxy-D-manno-octulosonic acid transferase
Reaction: α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA + CMP-β-Kdo = α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA + CMP
For diagram of Kdo4-Lipid IVA biosynthesis, click here
Glossary: (Kdo)2-lipid IVA = α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
(Kdo)3-lipid IVA = α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→8)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
CMP-β-Kdo = CMP-3-deoxy-β-D-manno-oct-2-ulopyranosylonate
Other name(s): Kdo transferase; waaA (gene name); kdtA (gene name); 3-deoxy-D-manno-oct-2-ulosonic acid transferase; 3-deoxy-manno-octulosonic acid transferase; (KDO)2-lipid IVA (2-8) 3-deoxy-D-manno-octulosonic acid transferase
Systematic name: CMP-3-deoxy-D-manno-oct-2-ulosonate:(Kdo)2-lipid IVA 3-deoxy-D-manno-oct-2-ulosonate transferase [(2→8) glycosidic bond-forming]
Comments: The enzymes from Chlamydia transfer three or more 3-deoxy-D-manno-oct-2-ulosonate residues and generate genus-specific epitopes.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lobau, S., Mamat, U., Brabetz, W. and Brade, H. Molecular cloning, sequence analysis, and functional characterization of the lipopolysaccharide biosynthetic gene kdtA encoding 3-deoxy-α-D-manno-octulosonic acid transferase of Chlamydia pneumoniae strain TW-183. Mol. Microbiol. 18 (1995) 391–399. [DOI] [PMID: 8748024]
2.  Mamat, U., Baumann, M., Schmidt, G. and Brade, H. The genus-specific lipopolysaccharide epitope of Chlamydia is assembled in C. psittaci and C. trachomatis by glycosyltransferases of low homology. Mol. Microbiol. 10 (1993) 935–941. [DOI] [PMID: 7523826]
3.  Belunis, C.J., Mdluli, K.E., Raetz, C.R. and Nano, F.E. A novel 3-deoxy-D-manno-octulosonic acid transferase from Chlamydia trachomatis required for expression of the genus-specific epitope. J. Biol. Chem. 267 (1992) 18702–18707. [PMID: 1382060]
[EC 2.4.99.14 created 2010, modified 2011]
 
 
EC 2.4.99.15     
Accepted name: (Kdo)3-lipid IVA (2-4) 3-deoxy-D-manno-octulosonic acid transferase
Reaction: α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA + CMP-β-Kdo = α-Kdo-(2→8)-[α-Kdo-(2→4)]-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA + CMP
For diagram of Kdo4-Lipid IVA biosynthesis, click here
Glossary: (Kdo)3-lipid IVA = α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→8)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
(Kdo)4-lipid IVA = α-Kdo-(2→8)-[α-Kdo-(2→4)]-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→8)-[(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)]-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
CMP-β-Kdo = CMP-3-deoxy-β-D-manno-oct-2-ulopyranosylonate
Other name(s): Kdo transferase; waaA (gene name); kdtA (gene name); 3-deoxy-D-manno-oct-2-ulosonic acid transferase; 3-deoxy-manno-octulosonic acid transferase; (KDO)3-lipid IVA (2-4) 3-deoxy-D-manno-octulosonic acid transferase
Systematic name: CMP-3-deoxy-D-manno-oct-2-ulosonate:(Kdo)3-lipid IVA 3-deoxy-D-manno-oct-2-ulosonate transferase [(2→4) glycosidic bond-forming]
Comments: The enzyme from Chlamydia psittaci transfers four Kdo residues to lipid A, forming a branched tetrasaccharide with the structure α-Kdo-(2,8)-[α-Kdo-(2,4)]-α-Kdo-(2,4)-α-Kdo (cf. EC 2.4.99.12 [lipid IVA 3-deoxy-D-manno-octulosonic acid transferase], EC 2.4.99.13 [(Kdo)-lipid IVA 3-deoxy-D-manno-octulosonic acid transferase], and EC 2.4.99.14 [(Kdo)2-lipid IVA (2-8) 3-deoxy-D-manno-octulosonic acid transferase]).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Brabetz, W., Lindner, B. and Brade, H. Comparative analyses of secondary gene products of 3-deoxy-D-manno-oct-2-ulosonic acid transferases from Chlamydiaceae in Escherichia coli K-12. Eur. J. Biochem. 267 (2000) 5458–5465. [DOI] [PMID: 10951204]
2.  Holst, O., Bock, K., Brade, L. and Brade, H. The structures of oligosaccharide bisphosphates isolated from the lipopolysaccharide of a recombinant Escherichia coli strain expressing the gene gseA [3-deoxy-D-manno-octulopyranosonic acid (Kdo) transferase] of Chlamydia psittaci 6BC. Eur. J. Biochem. 229 (1995) 194–200. [DOI] [PMID: 7744029]
[EC 2.4.99.15 created 2010, modified 2011]
 
 
EC 2.5.1.55     
Accepted name: 3-deoxy-8-phosphooctulonate synthase
Reaction: phosphoenolpyruvate + D-arabinose 5-phosphate + H2O = 3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
Other name(s): 2-dehydro-3-deoxy-D-octonate-8-phosphate D-arabinose-5-phosphate-lyase (pyruvate-phosphorylating); 2-dehydro-3-deoxy-phosphooctonate aldolase; 2-keto-3-deoxy-8-phosphooctonic synthetase; 3-deoxy-D-manno-octulosonate-8-phosphate synthase; 3-deoxy-D-mannooctulosonate-8-phosphate synthetase; 3-deoxyoctulosonic 8-phosphate synthetase; KDOP synthase; phospho-2-keto-3-deoxyoctonate aldolase
Systematic name: phosphoenolpyruvate:D-arabinose-5-phosphate C-(1-carboxyvinyl)transferase (phosphate-hydrolysing, 2-carboxy-2-oxoethyl-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9026-96-4
References:
1.  Levin, D.H. and Racker, E. Condensation of arabinose 5-phosphate and phosphorylenol pyruvate by 2-keto-3-deoxy-8-phosphooctonic acid synthetase. J. Biol. Chem. 234 (1959) 2532–25339. [PMID: 14416200]
2.  Krosky, D.J., Alm, R., Berg, M., Carmel, G., Tummino, P.J., Xu, B. and Yang, W. Helicobacter pylori 3-deoxy-D-manno-octulosonate-8-phosphate (KDO-8-P) synthase is a zinc-metalloenzyme. Biochim. Biophys. Acta 1594 (2002) 297–306. [DOI] [PMID: 11904225]
3.  Asojo, O., Friedman, J., Adir, N., Belakhov, V., Shoham, Y. and Baasov, T. Crystal structures of KDOP synthase in its binary complexes with the substrate phosphoenolpyruvate and with a mechanism-based inhibitor. Biochemistry 40 (2001) 6326–6334. [DOI] [PMID: 11371194]
[EC 2.5.1.55 created 1965 as EC 4.1.2.16, transferred 2002 to EC 2.5.1.55]
 
 
EC 2.6.1.109     
Accepted name: 8-amino-3,8-dideoxy-α-D-manno-octulosonate transaminase
Reaction: 8-amino-3,8-dideoxy-α-D-manno-octulosonate + 2-oxoglutarate = 8-dehydro-3-deoxy-α-D-manno-octulosonate + L-glutamate
Glossary: 3-deoxy-α-D-manno-octulosonate = Kdo
8-dehydro-3-deoxy-α-D-manno-octulosonate = (2R,4R,5R,6S)-2,4,5-trihydroxy-6-[(1S)-1-hydroxy-2-oxoethyl]oxane-2-carboxylate
Other name(s): kdnA (gene name)
Systematic name: 8-amino-3,8-dideoxy-α-D-manno-octulosonate:2-oxoglutarate aminotransferase
Comments: The enzyme, characterized from the bacterium Shewanella oneidensis, forms 8-amino-3,8-dideoxy-α-D-manno-octulosonate, an aminated form of Kdo found in lipopolysaccharides of members of the Shewanella genus. cf. EC 1.1.3.48, 3-deoxy-α-D-manno-octulosonate 8-oxidase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Gattis, S.G., Chung, H.S., Trent, M.S. and Raetz, C.R. The origin of 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) in the lipopolysaccharide of Shewanella oneidensis. J. Biol. Chem. 288 (2013) 9216–9225. [DOI] [PMID: 23413030]
[EC 2.6.1.109 created 2015]
 
 
EC 2.7.1.166     
Accepted name: 3-deoxy-D-manno-octulosonic acid kinase
Reaction: α-Kdo-(2→6)-lipid IVA + ATP = 4-O-phospho-α-Kdo-(2→6)-lipid IVA + ADP
Glossary: (Kdo)-lipid IVA = α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
(4-O-phospho-KDO)-lipid IVA = 4-O-phospho-α-Kdo-(2→6)-lipid IVA = (3-deoxy-4-O-phosphono-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
Other name(s): kdkA (gene name); Kdo kinase
Systematic name: ATP:(Kdo)-lipid IVA 3-deoxy-α-D-manno-oct-2-ulopyranose 4-phosphotransferase
Comments: The enzyme phosphorylates the 4-OH position of Kdo in (Kdo)-lipid IVA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Brabetz, W., Muller-Loennies, S. and Brade, H. 3-Deoxy-D-manno-oct-2-ulosonic acid (Kdo) transferase (WaaA) and kdo kinase (KdkA) of Haemophilus influenzae are both required to complement a waaA knockout mutation of Escherichia coli. J. Biol. Chem. 275 (2000) 34954–34962. [DOI] [PMID: 10952982]
2.  Harper, M., Boyce, J.D., Cox, A.D., St Michael, F., Wilkie, I.W., Blackall, P.J. and Adler, B. Pasteurella multocida expresses two lipopolysaccharide glycoforms simultaneously, but only a single form is required for virulence: identification of two acceptor-specific heptosyl I transferases. Infect. Immun. 75 (2007) 3885–3893. [DOI] [PMID: 17517879]
3.  White, K.A., Kaltashov, I.A., Cotter, R.J. and Raetz, C.R. A mono-functional 3-deoxy-D-manno-octulosonic acid (Kdo) transferase and a Kdo kinase in extracts of Haemophilus influenzae. J. Biol. Chem. 272 (1997) 16555–16563. [DOI] [PMID: 9195966]
4.  White, K.A., Lin, S., Cotter, R.J. and Raetz, C.R. A Haemophilus influenzae gene that encodes a membrane bound 3-deoxy-D-manno-octulosonic acid (Kdo) kinase. Possible involvement of kdo phosphorylation in bacterial virulence. J. Biol. Chem. 274 (1999) 31391–31400. [DOI] [PMID: 10531340]
[EC 2.7.1.166 created 2010, modified 2011]
 
 
EC 2.7.4.29     
Accepted name: Kdo2-lipid A phosphotransferase
Reaction: ditrans-octacis-undecaprenyl diphosphate + α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid A = ditrans-octacis-undecaprenyl phosphate + α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid A 1-diphosphate
Glossary: lipid A = 2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
lipid A 1-diphosphate =
2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl diphosphate
Other name(s): lipid A undecaprenyl phosphotransferase; LpxT; YeiU
Systematic name: ditrans-octacis-undecaprenyl diphosphate:α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid-A phosphotransferase
Comments: An inner-membrane protein. The activity of the enzyme is regulated by PmrA. In vitro the enzyme can use diacylglycerol 3-diphosphate as the phosphate donor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Touze, T., Tran, A.X., Hankins, J.V., Mengin-Lecreulx, D. and Trent, M.S. Periplasmic phosphorylation of lipid A is linked to the synthesis of undecaprenyl phosphate. Mol. Microbiol. 67 (2008) 264–277. [DOI] [PMID: 18047581]
2.  Herrera, C.M., Hankins, J.V. and Trent, M.S. Activation of PmrA inhibits LpxT-dependent phosphorylation of lipid A promoting resistance to antimicrobial peptides. Mol. Microbiol. 76 (2010) 1444–1460. [DOI] [PMID: 20384697]
[EC 2.7.4.29 created 2015]
 
 
EC 2.7.4.30      
Transferred entry: lipid A phosphoethanolamine transferase. Now EC 2.7.8.43, lipid A phosphoethanolamine transferase
[EC 2.7.4.30 created 2015, deleted 2016]
 
 
EC 2.7.7.38     
Accepted name: 3-deoxy-manno-octulosonate cytidylyltransferase
Reaction: CTP + 3-deoxy-D-manno-octulosonate = diphosphate + CMP-3-deoxy-D-manno-octulosonate
Other name(s): CMP-3-deoxy-D-manno-octulosonate pyrophosphorylase; 2-keto-3-deoxyoctonate cytidylyltransferase; 3-Deoxy-D-manno-octulosonate cytidylyltransferase; CMP-3-deoxy-D-manno-octulosonate synthetase; CMP-KDO synthetase; CTP:CMP-3-deoxy-D-manno-octulosonate cytidylyltransferase; cytidine monophospho-3-deoxy-D-manno-octulosonate pyrophosphorylase
Systematic name: CTP:3-deoxy-D-manno-octulosonate cytidylyltransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37278-28-7
References:
1.  Ghalambor, M.A. and Heath, E.C. The biosynthesis of cell wall lipopolysaccharide in Escherichia coli. IV. Purification and properties of cytidine monophosphate 3-deoxy-D-manno-octulosonate synthetase. J. Biol. Chem. 241 (1966) 3216–3221. [PMID: 5330266]
[EC 2.7.7.38 created 1972]
 
 
EC 2.7.7.65     
Accepted name: diguanylate cyclase
Reaction: 2 GTP = 2 diphosphate + cyclic di-3′,5′-guanylate
For diagram of cyclic di-3′,5′-guanylate biosynthesis and breakdown, click here
Glossary: cyclic di-3′,5′-guanylate = c-di-GMP = c-di-guanylate = cyclic-bis(3′→5′) dimeric GMP
Other name(s): DGC; PleD
Systematic name: GTP:GTP guanylyltransferase (cyclizing)
Comments: A GGDEF-domain-containing protein that requires Mg2+ or Mn2+ for activity. The enzyme can be activated by BeF3, a phosphoryl mimic, which results in dimerization [3]. Dimerization is required but is not sufficient for diguanylate-cyclase activity [3]. Cyclic di-3′,5′-guanylate is an intracellular signalling molecule that controls motility and adhesion in bacterial cells. It was first identified as having a positive allosteric effect on EC 2.4.1.12, cellulose synthase (UDP-forming) [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 146316-82-7
References:
1.  Ryjenkov, D.A., Tarutina, M., Moskvin, O.V. and Gomelsky, M. Cyclic diguanylate is a ubiquitous signaling molecule in bacteria: insights into biochemistry of the GGDEF protein domain. J. Bacteriol. 187 (2005) 1792–1798. [DOI] [PMID: 15716451]
2.  Méndez-Ortiz, M.M., Hyodo, M., Hayakawa, Y. and Membrillo-Hernández, J. Genome-wide transcriptional profile of Escherichia coli in response to high levels of the second messenger 3′,5′-cyclic diguanylic acid. J. Biol. Chem. 281 (2006) 8090–8099. [DOI] [PMID: 16418169]
3.  Paul, R., Abel, S., Wassmann, P., Beck, A., Heerklotz, H. and Jenal, U. Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization. J. Biol. Chem. 282 (2007) 29170–29177. [DOI] [PMID: 17640875]
[EC 2.7.7.65 created 2008]
 
 
EC 2.7.7.90     
Accepted name: 8-amino-3,8-dideoxy-manno-octulosonate cytidylyltransferase
Reaction: CTP + 8-amino-3,8-dideoxy-α-D-manno-octulosonate = diphosphate + CMP-8-amino-3,8-dideoxy-α-D-manno-octulosonate
Other name(s): kdsB (gene name, ambiguous)
Systematic name: CTP:8-amino-3,8-dideoxy-α-D-manno-octulosonate cytidylyltransferase
Comments: The enzyme, characterized from the bacterium Shewanella oneidensis MR-1, acts on the 8-aminated from of 3-deoxy-α-D-manno-octulosonate (Kdo). cf. EC 2.7.7.38, 3-deoxy-manno-octulosonate cytidylyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Gattis, S.G., Chung, H.S., Trent, M.S. and Raetz, C.R. The origin of 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) in the lipopolysaccharide of Shewanella oneidensis. J. Biol. Chem. 288 (2013) 9216–9225. [DOI] [PMID: 23413030]
[EC 2.7.7.90 created 2016]
 
 
EC 2.7.8.42     
Accepted name: Kdo2-lipid A phosphoethanolamine 7′′-transferase
Reaction: (1) diacylphosphatidylethanolamine + α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid A = diacylglycerol + 7-O-[2-aminoethoxy(hydroxy)phosphoryl]-α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid A
(2) diacylphosphatidylethanolamine + α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid IVA = diacylglycerol + 7-O-[2-aminoethoxy(hydroxy)phosphoryl]-α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid IVA
Glossary: lipid A = 2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
lipid IVA = 2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
Other name(s): eptB (gene name)
Systematic name: diacylphosphatidylethanolamine:α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid-A 7′′-phosphoethanolaminetransferase
Comments: The enzyme has been characterized from the bacterium Escherichia coli. It is activated by Ca2+ ions and is silenced by the sRNA MgrR.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kanipes, M.I., Lin, S., Cotter, R.J. and Raetz, C.R. Ca2+-induced phosphoethanolamine transfer to the outer 3-deoxy-D-manno-octulosonic acid moiety of Escherichia coli lipopolysaccharide. A novel membrane enzyme dependent upon phosphatidylethanolamine. J. Biol. Chem. 276 (2001) 1156–1163. [DOI] [PMID: 11042192]
2.  Reynolds, C.M., Kalb, S.R., Cotter, R.J. and Raetz, C.R. A phosphoethanolamine transferase specific for the outer 3-deoxy-D-manno-octulosonic acid residue of Escherichia coli lipopolysaccharide. Identification of the eptB gene and Ca2+ hypersensitivity of an eptB deletion mutant. J. Biol. Chem. 280 (2005) 21202–21211. [DOI] [PMID: 15795227]
3.  Moon, K., Six, D.A., Lee, H.J., Raetz, C.R. and Gottesman, S. Complex transcriptional and post-transcriptional regulation of an enzyme for lipopolysaccharide modification. Mol. Microbiol. 89 (2013) 52–64. [DOI] [PMID: 23659637]
[EC 2.7.8.42 created 2015]
 
 
EC 2.7.8.43     
Accepted name: lipid A phosphoethanolamine transferase
Reaction: (1) diacylphosphatidylethanolamine + lipid A = diacylglycerol + lipid A 1-(2-aminoethyl diphosphate)
(2) diacylphosphatidylethanolamine + lipid A = diacylglycerol + lipid A 4′-(2-aminoethyl diphosphate)
(3) diacylphosphatidylethanolamine + lipid A 1-(2-aminoethyl diphosphate) = diacylglycerol + lipid A 1,4′-bis(2-aminoethyl diphosphate)
Glossary: lipid A (Campylobacter jejuni) = 2,3-dideoxy-2,3-bis[(3R)-3-(hexadecanoyloxy)tetradecanamido]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
lipid A (Escherichia coli) =
2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
lipid A (Helicobacter pylori) = 2-deoxy-2-[(3R)-3-(octadecanoyloxy)octadecanamido]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxyhexadecanoyl]-2-[(3R)-3-hydroxyoctadecanamido]-α-D-glucopyranosyl phosphate
lipid A (Neisseria meningitidis) =
2-deoxy-3-O-[(3R)-3-hydroxydodecanoyl]-2-[(3R)-3-(dodecanoyloxy)tetradecanamido]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxydodecanoyl]-2-[(3R)-3-(dodecanoyloxy)tetradecanamido]-α-D-glucopyranosyl phosphate
lipid A 1-[(2-aminoethyl) diphosphate] = P1-(2-aminoethyl)
P2-(2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl) diphosphate
lipid A 1,4′-bis(2-aminoethyl diphosphate) = P1-(2-aminoethyl)
P2-(2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-(2-aminoethyldiphospho)-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl) diphosphate
Other name(s): lipid A PEA transferase; LptA
Systematic name: diacylphosphatidylethanolamine:lipid-A ethanolaminephosphotransferase
Comments: The enzyme adds one or two ethanolamine phosphate groups to lipid A giving a diphosphate, sometimes in combination with EC 2.4.2.43 (lipid IVA 4-amino-4-deoxy-L-arabinosyltransferase) giving products with 4-amino-4-deoxy-β-L-arabinose groups at the phosphates of lipid A instead of diphosphoethanolamine groups. It will also act on lipid IVA and Kdo2-lipid A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Tran, A.X., Karbarz, M.J., Wang, X., Raetz, C.R., McGrath, S.C., Cotter, R.J. and Trent, M.S. Periplasmic cleavage and modification of the 1-phosphate group of Helicobacter pylori lipid A. J. Biol. Chem. 279 (2004) 55780–55791. [DOI] [PMID: 15489235]
2.  Herrera, C.M., Hankins, J.V. and Trent, M.S. Activation of PmrA inhibits LpxT-dependent phosphorylation of lipid A promoting resistance to antimicrobial peptides. Mol. Microbiol. 76 (2010) 1444–1460. [DOI] [PMID: 20384697]
3.  Cullen, T.W. and Trent, M.S. A link between the assembly of flagella and lipooligosaccharide of the Gram-negative bacterium Campylobacter jejuni. Proc. Natl. Acad. Sci. USA 107 (2010) 5160–5165. [DOI] [PMID: 20194750]
4.  Anandan, A., Piek, S., Kahler, C.M. and Vrielink, A. Cloning, expression, purification and crystallization of an endotoxin-biosynthesis enzyme from Neisseria meningitidis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68 (2012) 1494–1497. [DOI] [PMID: 23192031]
5.  Wanty, C., Anandan, A., Piek, S., Walshe, J., Ganguly, J., Carlson, R.W., Stubbs, K.A., Kahler, C.M. and Vrielink, A. The structure of the neisserial lipooligosaccharide phosphoethanolamine transferase A (LptA) required for resistance to polymyxin. J. Mol. Biol. 425 (2013) 3389–3402. [DOI] [PMID: 23810904]
[EC 2.7.8.43 created 2015 as EC 2.7.4.30, transferred 2016 to EC 2.7.8.43]
 
 
EC 3.1.1.14     
Accepted name: chlorophyllase
Reaction: chlorophyll + H2O = phytol + chlorophyllide
For diagram of chlorophyll catabolism, click here
Other name(s): CLH; Chlase
Systematic name: chlorophyll chlorophyllidohydrolase
Comments: Chlorophyllase has been found in higher plants, diatoms, and in the green algae Chlorella [3]. This enzyme forms part of the chlorophyll degradation pathway and is thought to take part in de-greening processes such as fruit ripening, leaf senescence and flowering, as well as in the turnover and homeostasis of chlorophyll [4]. This enzyme acts preferentially on chlorophyll a but will also accept chlorophyll b and pheophytins as substrates [5]. Ethylene and methyl jasmonate, which are known to accelerate senescence in many species, can enhance the activity of the hormone-inducible form of this enzyme [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9025-96-1
References:
1.  Holden, M. The breakdown of chlorophyll by chlorophyllase. Biochem. J. 78 (1961) 359–364. [PMID: 13715233]
2.  Klein, A.O. and Vishniac, W. Activity and partial purification of chlorophyllase in aqueous systems. J. Biol. Chem. 236 (1961) 2544–2547. [PMID: 13756631]
3.  Tsuchiya, T., Ohta, H., Okawa, K., Iwamatsu, A., Shimada, H., Masuda, T. and Takamiya, K. Cloning of chlorophyllase, the key enzyme in chlorophyll degradation: finding of a lipase motif and the induction by methyl jasmonate. Proc. Natl. Acad. Sci. USA 96 (1999) 15362–15367. [DOI] [PMID: 10611389]
4.  Okazawa, A., Tango, L., Itoh, Y., Fukusaki, E. and Kobayashi, A. Characterization and subcellular localization of chlorophyllase from Ginkgo biloba. Z. Naturforsch. [C] 61 (2006) 111–117. [PMID: 16610227]
5.  Hörtensteiner, S. Chlorophyll degradation during senescence. Annu. Rev. Plant Biol. 57 (2006) 55–77. [DOI] [PMID: 16669755]
[EC 3.1.1.14 created 1961, modified 2007]
 
 
EC 3.1.3.84     
Accepted name: ADP-ribose 1′′-phosphate phosphatase
Reaction: ADP-D-ribose 1′′-phosphate + H2O = ADP-D-ribose + phosphate
Other name(s): POA1; Appr1p phosphatase; Poa1p; ADP-ribose 1′′-phosphate phosphohydrolase
Systematic name: ADP-D-ribose 1′′-phosphate phosphohydrolase
Comments: The enzyme is highly specific for ADP-D-ribose 1′′-phosphate. Involved together with EC 3.1.4.37, 2′,3′-cyclic-nucleotide 3′-phosphodiesterase, in the breakdown of adenosine diphosphate ribose 1′′,2′′-cyclic phosphate (Appr>p), a by-product of tRNA splicing.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Shull, N.P., Spinelli, S.L. and Phizicky, E.M. A highly specific phosphatase that acts on ADP-ribose 1′′-phosphate, a metabolite of tRNA splicing in Saccharomyces cerevisiae. Nucleic Acids Res. 33 (2005) 650–660. [DOI] [PMID: 15684411]
[EC 3.1.3.84 created 2011]
 
 
EC 3.1.4.52     
Accepted name: cyclic-guanylate-specific phosphodiesterase
Reaction: cyclic di-3′,5′-guanylate + H2O = 5′-phosphoguanylyl(3′→5′)guanosine
For diagram of cyclic di-3′,5′-guanylate biosynthesis and breakdown, click here
Glossary: c-di-GMP = c-di-guanylate = cyclic di-3′,5′-guanylate = cyclic-bis(3′→5′) dimeric GMP
Other name(s): cyclic bis(3′→5′)diguanylate phosphodiesterase; c-di-GMP-specific phosphodiesterase; c-di-GMP phosphodiesterase; phosphodiesterase (misleading); phosphodiesterase A1; PDEA1; VieA
Systematic name: cyclic bis(3′→5′)diguanylate 3′-guanylylhydrolase
Comments: Requires Mg2+ or Mn2+ for activity and is inhibited by Ca2+ and Zn2+. Contains a heme unit. This enzyme linearizes cyclic di-3′,5′-guanylate, the product of EC 2.7.7.65, diguanylate cyclase and an allosteric activator of EC 2.4.1.12, cellulose synthase (UDP-forming), rendering it inactive [1]. It is the balance between these two enzymes that determines the cellular level of c-di-GMP [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 338732-46-0
References:
1.  Chang, A.L., Tuckerman, J.R., Gonzalez, G., Mayer, R., Weinhouse, H., Volman, G., Amikam, D., Benziman, M. and Gilles-Gonzalez, M.A. Phosphodiesterase A1, a regulator of cellulose synthesis in Acetobacter xylinum, is a heme-based sensor. Biochemistry 40 (2001) 3420–3426. [DOI] [PMID: 11297407]
2.  Christen, M., Christen, B., Folcher, M., Schauerte, A. and Jenal, U. Identification and characterization of a cyclic di-GMP-specific phosphodiesterase and its allosteric control by GTP. J. Biol. Chem. 280 (2005) 30829–30837. [DOI] [PMID: 15994307]
3.  Schmidt, A.J., Ryjenkov, D.A. and Gomelsky, M. The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase: enzymatically active and inactive EAL domains. J. Bacteriol. 187 (2005) 4774–4781. [DOI] [PMID: 15995192]
4.  Tamayo, R., Tischler, A.D. and Camilli, A. The EAL domain protein VieA is a cyclic diguanylate phosphodiesterase. J. Biol. Chem. 280 (2005) 33324–33330. [DOI] [PMID: 16081414]
[EC 3.1.4.52 created 2008]
 
 
EC 3.1.4.59     
Accepted name: cyclic-di-AMP phosphodiesterase
Reaction: cyclic di-3′,5′-adenylate + H2O = 5′-O-phosphonoadenylyl-(3′→5′)-adenosine
Glossary: cyclic di-3′,5′-adenylate = cyclic bis(3′→5′)diadenylate
5′-O-phosphonoadenylyl-(3′→5′)-adenosine = pApA
Other name(s): gdpP (gene name)
Systematic name: cyclic bis(3′→5′)diadenylate 3′-adenylylhydrolase
Comments: The enzyme, described from Gram-positive bacteria, degrades the second messenger cyclic di-3′,5′-adenylate. It is a membrane-bound protein that contains a cytoplasmic facing Per-Arnt-Sim (PAS) domain, a modified GGDEF domain, and a DHH/DHHA1 domain, which confers the phosphodiesterase activity. Activity requires Mn2+ and is inhibited by pApA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Rao, F., See, R.Y., Zhang, D., Toh, D.C., Ji, Q. and Liang, Z.X. YybT is a signaling protein that contains a cyclic dinucleotide phosphodiesterase domain and a GGDEF domain with ATPase activity. J. Biol. Chem. 285 (2010) 473–482. [PMID: 19901023]
2.  Corrigan, R.M., Abbott, J.C., Burhenne, H., Kaever, V. and Grundling, A. c-di-AMP is a new second messenger in Staphylococcus aureus with a role in controlling cell size and envelope stress. PLoS Pathog. 7:e1002217 (2011). [PMID: 21909268]
3.  Griffiths, J.M. and O'Neill, A.J. Loss of function of the gdpP protein leads to joint β-lactam/glycopeptide tolerance in Staphylococcus aureus. Antimicrob. Agents Chemother. 56 (2012) 579–581. [PMID: 21986827]
4.  Bowman, L., Zeden, M.S., Schuster, C.F., Kaever, V. and Grundling, A. New insights into the cyclic di-adenosine monophosphate (c-di-AMP) degradation pathway and the requirement of the cyclic dinucleotide for acid stress resistance in Staphylococcus aureus. J. Biol. Chem. 291 (2016) 26970–26986. [PMID: 27834680]
[EC 3.1.4.59 created 2019]
 
 
EC 3.1.4.60     
Accepted name: pApA phosphodiesterase
Reaction: 5′-O-phosphonoadenylyl-(3′→5′)-adenosine + H2O = 2 AMP
Other name(s): pde2 (gene name); pApA hydrolase
Systematic name: 5′-O-phosphonoadenylyl-(3′→5′)-adenosine phosphohydrolase
Comments: The enzyme, characterized from the Gram-positive bacterium Staphylococcus aureus, is a cytoplasmic protein that contains a DHH/DHHA1 domain. It can act on cyclic di-3′,5′-adenylate with a much lower activity (cf. EC 3.1.4.59, cyclic-di-AMP phosphodiesterase). Activity requires Mn2+ and is inhibited by ppGpp.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bai, Y., Yang, J., Eisele, L.E., Underwood, A.J., Koestler, B.J., Waters, C.M., Metzger, D.W. and Bai, G. Two DHH subfamily 1 proteins in Streptococcus pneumoniae possess cyclic di-AMP phosphodiesterase activity and affect bacterial growth and virulence. J. Bacteriol. 195 (2013) 5123–5132. [PMID: 24013631]
2.  Ye, M., Zhang, J.J., Fang, X., Lawlis, G.B., Troxell, B., Zhou, Y., Gomelsky, M., Lou, Y. and Yang, X.F. DhhP, a cyclic di-AMP phosphodiesterase of Borrelia burgdorferi, is essential for cell growth and virulence. Infect. Immun. 82 (2014) 1840–1849. [PMID: 24566626]
3.  Tang, Q., Luo, Y., Zheng, C., Yin, K., Ali, M.K., Li, X. and He, J. Functional analysis of a c-di-AMP-specific phosphodiesterase MsPDE from Mycobacterium smegmatis. Int J Biol Sci 11 (2015) 813–824. [PMID: 26078723]
4.  Kuipers, K., Gallay, C., Martinek, V., Rohde, M., Martinkova, M., van der Beek, S.L., Jong, W.S., Venselaar, H., Zomer, A., Bootsma, H., Veening, J.W. and de Jonge, M.I. Highly conserved nucleotide phosphatase essential for membrane lipid homeostasis in Streptococcus pneumoniae. Mol. Microbiol. 101 (2016) 12–26. [PMID: 26691161]
5.  Bowman, L., Zeden, M.S., Schuster, C.F., Kaever, V. and Grundling, A. New insights into the cyclic di-adenosine monophosphate (c-di-AMP) degradation pathway and the requirement of the cyclic dinucleotide for acid stress resistance in Staphylococcus aureus. J. Biol. Chem. 291 (2016) 26970–26986. [PMID: 27834680]
[EC 3.1.4.60 created 2019]
 
 
EC 3.2.1.91     
Accepted name: cellulose 1,4-β-cellobiosidase (non-reducing end)
Reaction: Hydrolysis of (1→4)-β-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non-reducing ends of the chains
Other name(s): exo-cellobiohydrolase; β-1,4-glucan cellobiohydrolase; β-1,4-glucan cellobiosylhydrolase; 1,4-β-glucan cellobiosidase; exoglucanase; avicelase; CBH 1; C1 cellulase; cellobiohydrolase I; cellobiohydrolase; exo-β-1,4-glucan cellobiohydrolase; 1,4-β-D-glucan cellobiohydrolase; cellobiosidase
Systematic name: 4-β-D-glucan cellobiohydrolase (non-reducing end)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37329-65-0
References:
1.  Berghem, L.E.R. and Pettersson, L.G. The mechanism of enzymatic cellulose degradation. Purification of a cellulolytic enzyme from Trichoderma viride active on highly ordered cellulose. Eur. J. Biochem. 37 (1973) 21–30. [DOI] [PMID: 4738092]
2.  Eriksson, K.E. and Pettersson, B. Extracellular enzyme system utilized by the fungus Sporotrichum pulverulentum (Chrysosporium lignorum) for the breakdown of cellulose. 3. Purification and physico-chemical characterization of an exo-1,4-β-glucanase. Eur. J. Biochem. 51 (1975) 213–218. [DOI] [PMID: 235428]
3.  Halliwell, G., Griffin, M. and Vincent, R. The role of component C1 in cellulolytic systems. Biochem. J. 127 (1972) 43P. [PMID: 5076675]
[EC 3.2.1.91 created 1976, modified 2011]
 
 
EC 3.2.1.124     
Accepted name: 3-deoxy-2-octulosonidase
Reaction: Endohydrolysis of the β-ketopyranosidic linkages of 3-deoxy-D-manno-2-octulosonate in capsular polysaccharides
Other name(s): 2-keto-3-deoxyoctonate hydrolase; octulosylono hydrolase; octulofuranosylono hydrolase; octulopyranosylonohydrolase
Systematic name: capsular-polysaccharide 3-deoxy-D-manno-2-octulosonohydrolase
Comments: The enzyme from a bacteriophage catalyses the depolymerization of capsular polysaccharides containing 3-deoxy-2-octulosonide in the cell wall of Escherichia coli.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 103171-48-8
References:
1.  Altmann, F., Kwiatkowski, B., Stirm, S., März, L. and Unger, F.M. A bacteriophage-associated glycanase cleaving β-pyranosidic linkages of 3-deoxy-D-manno-2-octulosonic acid (KDO). Biochem. Biophys. Res. Commun. 136 (1986) 329–335. [DOI] [PMID: 3707579]
[EC 3.2.1.124 created 1989]
 
 
EC 3.2.1.144     
Accepted name: 3-deoxyoctulosonase
Reaction: 3-deoxyoctulosonyl-lipopolysaccharide + H2O = 3-deoxyoctulosonic acid + lipopolysaccharide
Other name(s): α-Kdo-ase
Systematic name: 3-deoxyoctulosonyl-lipopolysaccharide hydrolase
Comments: Releases Kdo (α- and β-linked 3-deoxy-D-manno-octulosonic acid) from different lipopolysaccharides, including Re-LPS from Escherichia coli and Salmonella, Rd-LPS from S. minnesota, and de-O-acyl-re-LPS. 4-Methylumbelliferyl-α-Kdo (α-Kdo-OMec) is also a substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 199128-67-1
References:
1.  Li, Y.T., Wang, L.X., Pavlova, N.V., Li, S.C. and Lee, Y.C. α-KDOase activity in oyster and synthesis of α- and β-4-methylumbelliferyl ketosides of 3-deoxy-D-manno-octulosonic acid (KDO). J. Biol. Chem. 272 (1997) 26419–26424. [DOI] [PMID: 9334217]
[EC 3.2.1.144 created 2000]
 
 
EC 3.4.19.9     
Accepted name: folate γ-glutamyl hydrolase
Reaction: tetrahydropteroyl-(γ-glutamyl)n + (n-1) H2O = 5,6,7,8-tetrahydrofolate + (n-1) L-glutamate
Other name(s): GGH (gene name); conjugase; folate conjugase; lysosomal γ-glutamyl carboxypeptidase; γ-Glu-X carboxypeptidase; pteroyl-poly-γ-glutamate hydrolase; carboxypeptidase G; folic acid conjugase; poly(γ-glutamic acid) endohydrolase; polyglutamate hydrolase; poly(glutamic acid) hydrolase II; pteroylpoly-γ-glutamyl hydrolase; γ-glutamyl hydrolase
Systematic name: tetrahydropteroyl-poly-γ-glutamyl γ-glutamyl hydrolase
Comments: The enzyme, which occurs only in animals and plants, can be either endo- and/or exopeptidase. It acts on tetrahydropteroyl polyglutamates and their modified forms, as well as the polyglutamates of the folate breakdown product N-(4-aminobenzoyl)-L-glutamate (pABA-Glu). The initial cleavage may release either monoglutamate or poly-γ-glutamate of two or more residues, depending on the specific enzyme. For example, GGH1 from the plant Arabidopsis thaliana cleaves pentaglutamates, mainly to di- and triglutamates, whereas GGH2 from the same organism yields mainly monoglutamates. The enzyme is lysosomal (and secreted) in animals and vacuolar in plants.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, MEROPS, PDB, CAS registry number: 9074-87-7
References:
1.  McGuire, J.J. and Coward, J.K. Pteroylpolyglutamates: biosynthesis, degradation and function.. In: Blakley, R.L. and Benkovic, S.J. (Ed.), Folates and Pterins, John Wiley and Sons, New York, 1984, pp. 135–191.
2.  Wang, Y., Nimec, Z., Ryan, T.J., Dias, J.A. and Galivan, J. The properties of the secreted γ-glutamyl hydrolases from H35 hepatoma cells. Biochim. Biophys. Acta 1164 (1993) 227–235. [DOI] [PMID: 8343522]
3.  Yao, R., Rhee, M.S. and Galivan, J. Effects of γ-glutamyl hydrolase on folyl and antifolylpolyglutamates in cultured H35 hepatoma cells. Mol. Pharmacol. 48 (1995) 505–511. [PMID: 7565632]
4.  Yao, R., Schneider, E., Ryan, T.J. and Galivan, J. Human γ-glutamyl hydrolase: cloning and characterization of the enzyme expressed in vitro. Proc. Natl. Acad. Sci. USA 93 (1996) 10134–10138. [DOI] [PMID: 8816764]
5.  Yao, R., Nimec, Z., Ryan, T.J. and Galivan, J. Identification, cloning, and sequencing of a cDNA coding for rat γ-glutamyl hydrolase. J. Biol. Chem. 271 (1996) 8525–8528. [DOI] [PMID: 8621474]
6.  Orsomando, G., de la Garza, R.D., Green, B.J., Peng, M., Rea, P.A., Ryan, T.J., Gregory, J.F., 3rd and Hanson, A.D. Plant γ-glutamyl hydrolases and folate polyglutamates: characterization, compartmentation, and co-occurrence in vacuoles. J. Biol. Chem. 280 (2005) 28877–28884. [PMID: 15961386]
7.  Akhtar, T.A., McQuinn, R.P., Naponelli, V., Gregory, J.F., 3rd, Giovannoni, J.J. and Hanson, A.D. Tomato γ-glutamylhydrolases: expression, characterization, and evidence for heterodimer formation. Plant Physiol. 148 (2008) 775–785. [PMID: 18757550]
[EC 3.4.19.9 created 1972 as EC 3.4.12.10, transferred 1978 to EC 3.4.22.12, transferred 1992 to EC 3.4.19.9, modified 1997, modified 2018]
 
 
EC 3.4.21.97     
Accepted name: assemblin
Reaction: Cleaves -Ala┼Ser- and -Ala┼Ala- bonds in the scaffold protein
Comments: Involved in the breakdown of the scaffold protein during the late stages of assembly of the herpes-virus virion. Inhibited by diisopropyl fluorophosphate. Type example of peptidase family S21. Catalytic residues are His, Ser, His, a combination not known for any other peptidase, and the protein fold also is unique. Known from herpes viruses of several types, cytomegalovirus, Epstein-Barr virus and human herpesvirus 3
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, MEROPS, PDB, CAS registry number: 139691-88-6
References:
1.  Chen, P., Tsuge, H., Almassy, R.J., Gribskov, C.L., Katoh, S., Vanderpool, D.L., Margosiak, S.A., Pinko, C., Matthews, D.A. and Kan, C.C. Structure of the human cytomegalovirus protease catalytic domain reveals a novel serine protease fold and catalytic triad. Cell 86 (1996) 477–483. [DOI] [PMID: 8797829]
2.  Darke, P.L. Herpesvirus assemblin. In: Barrett, A.J., Rawlings, N.D. and Woessner, J.F. (Ed.), Handbook of Proteolytic Enzymes, Academic Press, London, 1998, pp. 470–472.
[EC 3.4.21.97 created 2000]
 
 
EC 3.5.1.7     
Accepted name: ureidosuccinase
Reaction: N-carbamoyl-L-aspartate + H2O = L-aspartate + CO2 + NH3
Systematic name: N-carbamoyl-L-aspartate amidohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9024-81-1
References:
1.  Lieberman, I. and Kornberg, A. Enzymatic synthesis and breakdown of a pyrimidine, orotic acid. III. Ureidosuccinase. J. Biol. Chem. 212 (1955) 909–920. [PMID: 14353892]
[EC 3.5.1.7 created 1961]
 
 
EC 3.5.1.29     
Accepted name: 2-(acetamidomethylene)succinate hydrolase
Reaction: 2-(acetamidomethylene)succinate + 2 H2O = acetate + succinate semialdehyde + NH3 + CO2
Other name(s): α-(N-acetylaminomethylene)succinic acid hydrolase
Systematic name: 2-(acetamidomethylene)succinate amidohydrolase (deaminating, decarboxylating)
Comments: Involved in the degradation of pyridoxin in Pseudomonas.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 37289-09-1
References:
1.  Huynh, M.S. and Snell, E.E. Enzymes of vitamin B6 degradation. Purification and properties of two N-acetylamidohydrolases. J. Biol. Chem. 260 (1985) 2379–2383. [PMID: 3972793]
2.  Nyns, E.J., Zach, D. and Snell, E.E. The bacterial oxidation of vitamin B6. 8. Enzymatic breakdown of α-(N-acetylaminomethylene) succinic acid. J. Biol. Chem. 244 (1969) 2601–2605. [PMID: 5769993]
[EC 3.5.1.29 created 1972]
 
 
EC 3.5.2.3     
Accepted name: dihydroorotase
Reaction: (S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate
For diagram of pyrimidine biosynthesis, click here
Other name(s): carbamoylaspartic dehydrase; dihydroorotate hydrolase
Systematic name: (S)-dihydroorotate amidohydrolase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9024-93-5
References:
1.  Cooper, C. and Wilson, D.W. Biosynthesis of pyrimidines. Fed. Proc. 13 (1954) 194.
2.  Lieberman, I. and Kornberg, A. Enzymatic synthesis and breakdown of a pyrimidine, orotic acid. II. Dihydroorotic acid, ureidosuccinic acid, and 5-carboxymethylhydantoin. J. Biol. Chem. 207 (1954) 911–924. [PMID: 13163076]
[EC 3.5.2.3 created 1961]
 
 


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