KEGG   ENZYME: 4.2.1.168
Entry
EC 4.2.1.168                Enzyme                                 
Name
GDP-4-dehydro-6-deoxy-alpha-D-mannose 3-dehydratase;
colD (gene name)
Class
Lyases;
Carbon-oxygen lyases;
Hydro-lyases
Sysname
GDP-4-dehydro-alpha-D-rhamnose 3-hydro-lyase
Reaction(IUBMB)
GDP-4-dehydro-alpha-D-rhamnose + L-glutamate = GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose + 2-oxoglutarate + NH3 (overall reaction) [RN:R11409];
(1a) GDP-4-dehydro-alpha-D-rhamnose + L-glutamate = 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol] + 2-oxoglutarate + H2O;
(1b) 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol] = 2-GDP-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] (spontaneous);
(1c) GDP-2-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] + H2O = GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose + NH3 (spontaneous)
Reaction(KEGG)
R11409
Substrate
GDP-4-dehydro-alpha-D-rhamnose [CPD:C01222];
L-glutamate [CPD:C00025];
2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol];
GDP-2-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol];
H2O [CPD:C00001]
Product
GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose [CPD:C20612];
2-oxoglutarate [CPD:C00026];
NH3 [CPD:C00014];
2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol];
H2O [CPD:C00001];
2-GDP-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] (spontaneous)
Comment
This enzyme, involved in beta-L-colitose biosynthesis, is a unique vitamin-B6-dependent enzyme. In the first step of catalysis, the bound pyridoxal phosphate (PLP) cafactor is transaminated to the pyridoxamine 5'-phosphate (PMP) form of vitamin B6, using L-glutamate as the amino group donor. The PMP cofactor then forms a Schiff base with the sugar substrate and the resulting adduct undergoes a 1,4-dehydration to eliminate the 3-OH group. Hydrolysis of the product from the enzyme restores the PLP cofactor and results in the release of an unstable enamine intermediate. This intermediate tautomerizes to form an imine form, which hydrolyses spontaneously, releasing ammonia and forming the final product.
History
EC 4.2.1.168 created 2016
Pathway
ec00541  O-Antigen nucleotide sugar biosynthesis
ec01100  Metabolic pathways
Orthology
K21131  GDP-4-dehydro-6-deoxy-alpha-D-mannose 3-dehydratase
Genes
EOIECO111_2760(wbdK)
EOKG2583_2551(wbdK)
ELRECO55CA74_12270
YSIBF17_13445
YASN0H69_17375
VGIMID13_00925
SPSHFM037_09965
CPSCPS_4201
PTDPTET_a0496
MOZMoryE10_16090
CASPNQ535_24820
IFNGM661_06815
RMLFF011L_51340(arnB)
MAQILDL77_09085
 » show all
Reference
1  [PMID:15610039]
  Authors
Alam J, Beyer N, Liu HW
  Title
Biosynthesis of colitose: expression, purification, and mechanistic characterization of GDP-4-keto-6-deoxy-D-mannose-3-dehydrase (ColD) and GDP-L-colitose synthase (ColC).
  Journal
Biochemistry 43:16450-60 (2004)
DOI:10.1021/bi0483763
  Sequence
Reference
2  [PMID:17997582]
  Authors
Cook PD, Holden HM
  Title
A structural study of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: caught in the act of geminal diamine formation.
  Journal
Biochemistry 46:14215-24 (2007)
DOI:10.1021/bi701686s
  Sequence
Other DBs
ExplorEnz - The Enzyme Database: 4.2.1.168
IUBMB Enzyme Nomenclature: 4.2.1.168
ExPASy - ENZYME nomenclature database: 4.2.1.168
BRENDA, the Enzyme Database: 4.2.1.168

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