The Enzyme Database

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EC 1.14.11.52     
Accepted name: validamycin A dioxygenase
Reaction: validamycin A + 2-oxoglutarate + O2 = validamycin B + succinate + CO2
For diagram of validamycin biosynthesis, click here
Glossary: validamycin A = (1R,2R,3S,4S,6R)-2,3-dihydroxy-6-(hydroxymethyl)-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}cyclohexyl β-D-glucopyranoside
validamycin B = (1R,2R,3S,4S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}cyclohexyl β-D-glucopyranoside
Other name(s): vldW (gene name)
Systematic name: validamycin-A,2-oxoglutarate:oxygen oxidoreductase (6′-hydroxylating)
Comments: The enzyme was characterized from the bacterium Streptomyces hygroscopicus subsp. limoneus. Requires Fe2+.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Almabruk, K.H., Asamizu, S., Chang, A., Varghese, S.G. and Mahmud, T. The α-ketoglutarate/Fe(II)-dependent dioxygenase VldW is responsible for the formation of validamycin B. ChemBioChem 13 (2012) 2209–2211. [DOI] [PMID: 22961651]
[EC 1.14.11.52 created 2016]
 
 
EC 2.4.1.338     
Accepted name: validoxylamine A glucosyltransferase
Reaction: UDP-α-D-glucose + validoxylamine A = UDP + validamycin A
For diagram of validamycin biosynthesis, click here
Glossary: validoxylamine A = (1S,2S,3R,6S)-4-(hydroxymethyl)-6-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}cyclohex-4-ene-1,2,3-triol
Other name(s): vldK (gene name); valG (gene name)
Systematic name: UDP-α-D-glucose:validoxylamine-A 4′-O-glucosyltransferase
Comments: The enzyme, characterized from the bacterium Streptomyces hygroscopicus subsp. limoneus, catalyses the ultimate step in the biosynthesis of the antifungal agent validamycin A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bai, L., Li, L., Xu, H., Minagawa, K., Yu, Y., Zhang, Y., Zhou, X., Floss, H.G., Mahmud, T. and Deng, Z. Functional analysis of the validamycin biosynthetic gene cluster and engineered production of validoxylamine A. Chem. Biol. 13 (2006) 387–397. [DOI] [PMID: 16632251]
2.  Xu, H., Minagawa, K., Bai, L., Deng, Z. and Mahmud, T. Catalytic analysis of the validamycin glycosyltransferase (ValG) and enzymatic production of 4′′-epi-validamycin A. J Nat Prod 71 (2008) 1233–1236. [DOI] [PMID: 18563934]
[EC 2.4.1.338 created 2016]
 
 
EC 2.5.1.135     
Accepted name: validamine 7-phosphate valienyltransferase
Reaction: GDP-valienol + validamine 7-phosphate = validoxylamine A 7′-phosphate + GDP
For diagram of validamycin biosynthesis, click here
Glossary: valienol = (1S,2S,3S,4R)-5-(hydroxymethyl)cyclohex-5-ene-1,2,3,4-tetrol
validamine = (1R,2S,3S,4S,6R)-4-amino-6-(hydroxymethyl)cyclohexane-1,2,3-triol
Other name(s): vldE (gene name); valL (gene name)
Systematic name: GDP-valienol:validamine 7-phosphate valienyltransferase
Comments: The enzyme, characterized from several Streptomyces strains, is involved in the biosynthesis of the antifungal agent validamycin A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Asamizu, S., Yang, J., Almabruk, K.H. and Mahmud, T. Pseudoglycosyltransferase catalyzes nonglycosidic C-N coupling in validamycin a biosynthesis. J. Am. Chem. Soc. 133 (2011) 12124–12135. [DOI] [PMID: 21766819]
2.  Zheng, L., Zhou, X., Zhang, H., Ji, X., Li, L., Huang, L., Bai, L. and Zhang, H. Structural and functional analysis of validoxylamine A 7′-phosphate synthase ValL involved in validamycin A biosynthesis. PLoS One 7:e32033 (2012). [DOI] [PMID: 22384130]
3.  Cavalier, M.C., Yim, Y.S., Asamizu, S., Neau, D., Almabruk, K.H., Mahmud, T. and Lee, Y.H. Mechanistic insights into validoxylamine A 7′-phosphate synthesis by VldE using the structure of the entire product complex. PLoS One 7:e44934 (2012). [DOI] [PMID: 23028689]
[EC 2.5.1.135 created 2016]
 
 
EC 2.7.1.214     
Accepted name: C7-cyclitol 7-kinase
Reaction: (1) ATP + valienone = ADP + valienone 7-phosphate
(2) ATP + validone = ADP + validone 7-phosphate
Glossary: valienone = (4R,5S,6R)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-one
validone = (2R,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexan-1-one
Other name(s): valC (gene name); vldC (gene name)
Systematic name: ATP:C7-cyclitol 7-phosphotransferase
Comments: The enzyme, characterized from the bacterium Streptomyces hygroscopicus var. jinggangensis, is involved in the biosynthesis of the antifungal agent validamycin A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Minagawa, K., Zhang, Y., Ito, T., Bai, L., Deng, Z. and Mahmud, T. ValC, a new type of C7-Cyclitol kinase involved in the biosynthesis of the antifungal agent validamycin A. ChemBioChem 8 (2007) 632–641. [DOI] [PMID: 17335096]
[EC 2.7.1.214 created 2016]
 
 
EC 2.7.7.91     
Accepted name: valienol-1-phosphate guanylyltransferase
Reaction: GTP + valienol 1-phosphate = diphosphate + GDP-valienol
For diagram of validamycin biosynthesis, click here
Glossary: valienol 1-phosphate = (1S,4R,5S,6R)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl phosphate
Other name(s): vldB (gene name)
Systematic name: GTP:valienol 1-phosphate guanylyltransferase
Comments: The enzyme, characterized from the bacterium Streptomyces hygroscopicus subsp. limoneus, is involved in the biosynthesis of the antifungal agent validamycin A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yang, J., Xu, H., Zhang, Y., Bai, L., Deng, Z. and Mahmud, T. Nucleotidylation of unsaturated carbasugar in validamycin biosynthesis. Org. Biomol. Chem. 9 (2011) 438–449. [DOI] [PMID: 20981366]
2.  Asamizu, S., Yang, J., Almabruk, K.H. and Mahmud, T. Pseudoglycosyltransferase catalyzes nonglycosidic C-N coupling in validamycin a biosynthesis. J. Am. Chem. Soc. 133 (2011) 12124–12135. [DOI] [PMID: 21766819]
[EC 2.7.7.91 created 2016]
 
 
EC 3.1.3.101     
Accepted name: validoxylamine A 7′-phosphate phosphatase
Reaction: validoxylamine A 7′-phosphate + H2O = validoxylamine A + phosphate
For diagram of validamycin biosynthesis, click here
Glossary: validoxylamine A = (1S,2S,3R,6S)-4-(hydroxymethyl)-6-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}cyclohex-4-ene-1,2,3-triol
Other name(s): vldH (gene name)
Systematic name: validoxylamine-A 7′-phosphate phosphohydrolase
Comments: The enzyme, characterized from the bacterium Streptomyces hygroscopicus subsp. limoneus, is involved in the biosynthesis of the antifungal agent validamycin A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Asamizu, S., Yang, J., Almabruk, K.H. and Mahmud, T. Pseudoglycosyltransferase catalyzes nonglycosidic C-N coupling in validamycin a biosynthesis. J. Am. Chem. Soc. 133 (2011) 12124–12135. [DOI] [PMID: 21766819]
[EC 3.1.3.101 created 2016]
 
 
EC 4.2.3.152     
Accepted name: 2-epi-5-epi-valiolone synthase
Reaction: α-D-sedoheptulopyranose 7-phosphate = 2-epi-5-epi-valiolone + phosphate
For diagram of valiolone biosynthesis, click here
Glossary: 2-epi-5-epi-valiolone = (2S,3S,4S,5R)-2,3,4,5-tetrahydroxy-5-(hydroxymethyl)cyclohexan-1-one
Other name(s): AcbC; ValA; CetA; SalQ; C7-cyclitol synthase
Systematic name: α-D-sedoheptulopyranose-7-phosphate phosphate-lyase (cyclizing; 2-epi-5-epi-valiolone-forming)
Comments: The enzyme is highly specific for α-D-sedoheptulopyranose 7-phosphate. It requires a divalent metal ion (Zn2+ or Co2+) and an NAD+ cofactor, which is transiently reduced during the reaction. The enzyme is involved in the biosynthesis of C7N-aminocyclitol natural products, such as the valienamine moiety of the antidiabetic drug acarbose and the crop protectant validamycin A. cf. EC 4.2.3.155, 2-epi-valiolone synthase and EC 4.2.3.154, demethyl-4-deoxygadusol synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Stratmann, A., Mahmud, T., Lee, S., Distler, J., Floss, H.G. and Piepersberg, W. The AcbC protein from Actinoplanes species is a C7-cyclitol synthase related to 3-dehydroquinate synthases and is involved in the biosynthesis of the α-glucosidase inhibitor acarbose. J. Biol. Chem. 274 (1999) 10889–10896. [DOI] [PMID: 10196166]
2.  Yu, Y., Bai, L., Minagawa, K., Jian, X., Li, L., Li, J., Chen, S., Cao, E., Mahmud, T., Floss, H.G., Zhou, X. and Deng, Z. Gene cluster responsible for validamycin biosynthesis in Streptomyces hygroscopicus subsp. jinggangensis 5008. Appl. Environ. Microbiol. 71 (2005) 5066–5076. [DOI] [PMID: 16151088]
3.  Wu, X., Flatt, P.M., Schlorke, O., Zeeck, A., Dairi, T. and Mahmud, T. A comparative analysis of the sugar phosphate cyclase superfamily involved in primary and secondary metabolism. ChemBioChem 8 (2007) 239–248. [DOI] [PMID: 17195255]
4.  Choi, W.S., Wu, X., Choeng, Y.H., Mahmud, T., Jeong, B.C., Lee, S.H., Chang, Y.K., Kim, C.J. and Hong, S.K. Genetic organization of the putative salbostatin biosynthetic gene cluster including the 2-epi-5-epi-valiolone synthase gene in Streptomyces albus ATCC 21838. Appl. Microbiol. Biotechnol. 80 (2008) 637–645. [DOI] [PMID: 18648803]
5.  Kean, K.M., Codding, S.J., Asamizu, S., Mahmud, T. and Karplus, P.A. Structure of a sedoheptulose 7-phosphate cyclase: ValA from Streptomyces hygroscopicus. Biochemistry 53 (2014) 4250–4260. [DOI] [PMID: 24832673]
[EC 4.2.3.152 created 2015, modified 2016]
 
 
EC 4.3.3.1     
Accepted name: 3-ketovalidoxylamine C-N-lyase
Reaction: 4-nitrophenyl-3-ketovalidamine = 4-nitroaniline + 5-D-(5/6)-5-C-(hydroxymethyl)-2,6-dihydroxycyclohex-2-en-1-one
Other name(s): 3-ketovalidoxylamine A C-N-lyase; p-nitrophenyl-3-ketovalidamine p-nitroaniline lyase; 4-nitrophenyl-3-ketovalidamine 4-nitroaniline-lyase
Systematic name: 4-nitrophenyl-3-ketovalidamine 4-nitroaniline-lyase [5-D-(5/6)-5-C-(hydroxymethyl)-2,6-dihydroxycyclohex-2-en-1-one-forming]
Comments: Requires Ca2+. Eliminates 4-nitroaniline from 4-nitrophenyl-3-ketovalidamine, or 4-nitrophenol from 4-nitrophenyl-α-D-3-dehydroglucoside. Involved in the degradation of the fungicide validamycin A by Flavobacterium saccharophilum.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 99889-98-2
References:
1.  Asano, N., Takeuchi, M., Ninomiya, K., Kameda, Y. and Matsui, K. Microbial degradation of validamycin A by Flavobacterium saccharophilum. Enzymatic cleavage of C-N linkage in validoxylamine A. J. Antibiot. 37 (1984) 859–867. [PMID: 6548220]
2.  Takeuchi, M., Asano, N., Kameda, Y. and Matsui, K. Purification and properties of 3-ketovalidoxylamine A C-N lyase from Flavobacterium saccharophilum. J. Biochem. (Tokyo) 98 (1985) 1631–1638. [PMID: 4093450]
[EC 4.3.3.1 created 1989]
 
 


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