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  Biosynthesis of various nucleotide sugars
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
AAPCQG404_01580
VGIMID13_00925
PSKU771_09390
SPSHFM037_09965
CPSCPS_4201
PTDPTET_a0496
PSHOKQ246_01880
FRFLO80_08560
FRLFIP56_03870
FGUSD28_06630
HMARHVMH_0583
MARDIBG28_16570
AJPAMJAP_0618(rfbH)
VOXLCH97_15635
PVEUC34_23520
PANXOYT13_23735
ASAHAVXHC19_09740
AAAAcav_0931
XYKGT347_20605
MMBMmol_1027
SLTSlit_2900
NIVJY500_12270
EADOV14_a0818
SHINLHJ69_15680
CHELAL346_24230
PPHRAPZ00_05965
LAPACP90_26740
JOVP8627_10175
PHAEN1037_21650
SUAMBOO69_17655
ROMEI983_00895
ROHFIU89_02675(arnB)
RPHCRZ517_04225
RRLRZS32_004660
PDEPden_1296
PZHCX676_04245
PAROCUV01_17505
PAMNJCM7685_1751
PPANESD82_04570
PSEWJHW44_16930
PALPJHW40_06890
PVERE3U25_05760
PFEOE3U26_21225
SEDIEBB79_24535
FRBAB6B37_14205
SRADLLW23_09455
SNOSK8P63_01925
SPNBO3305_22955
SPMIK663_12810
AFLVQQW98_00955
ALIAZOLI_p60037
ABQABAZ39_33090
ATIAL072_31845
AZMDM194_26675
AZZDEW08_29840
ADJACIU1J_15920
MAGNWV31_16790
FERFNB15_03155
MAGamb0793 amb1072
MGMMmc1_0616
HADCDV25_00555
SUASaut_1506
SMAXFJR03_06785
SAQTGJV85_09665
CJQUC78_1368(arnB)
CJDJJD26997_0710
CLRUPTC16701_0314
CLNUPTC3659_0324
CCCG157_03205
CCQN149_1087
CCOFVC76_05625(arnB)
CCUNCCUN_1145
CLXCLAN_0165
CAMZCVIC12175_0169
CUXCUP3940_1447
CDEVCIGN_0125
SDLSdel_1788
ACREACRYA_0760
ANTArnit_2926
AMYTAMYT_0707
BDQCIK05_07095
SNGSNE_A16740(rfbH)
KSTKSMBR1_2294(rfbE_4)
BHPBHAMNSH16_06895
MSILMETEAL_02510
BLQL21SP5_01961(pseC)
MBASALGA_0233
EVIEchvi_4396
CAPFFOC45_00350
TMARMARIT_3152
WFUAXE80_11245
OAQDZC78_10410
MUREQY75_13175
MAQILDL77_09085
FBQD1817_12920
CPBCphamn1_1930
LFILFML04_1775
NVAG3M78_07670
PAUNMJA45_22840
ELIMB2M23_15755
LACYA4V08_21435
CASPNQ535_24820
ECLFQMP25_33390
IFNGM661_06815
HPRFHLPR_26900
AGMDCE93_09755
ALAVMTO99_01530
CHREIE160_10025
SALCC2138_02970
SALDFVA74_04140
PLAPEAO79_16755
PFLUBWO91_13105
GLNF1C58_03080
CELHGXP71_09765
CDONKKR89_11895
THERY592_04200
PSYTDSAG12_01852
 » 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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