GM4D_YERE8
ID GM4D_YERE8 Reviewed; 372 AA.
AC Q56872; A1JN62;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 20-MAR-2007, sequence version 2.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=GDP-mannose 4,6-dehydratase {ECO:0000255|HAMAP-Rule:MF_00955};
DE EC=4.2.1.47 {ECO:0000255|HAMAP-Rule:MF_00955};
DE AltName: Full=GDP-D-mannose dehydratase {ECO:0000255|HAMAP-Rule:MF_00955};
GN Name=gmd {ECO:0000255|HAMAP-Rule:MF_00955}; OrderedLocusNames=YE3075;
OS Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 /
OS 8081).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=393305;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PATHWAY.
RX PubMed=8932701; DOI=10.1099/13500872-142-2-277;
RA Zhang L., Toivanen P., Skurnik M.;
RT "The gene cluster directing O-antigen biosynthesis in Yersinia
RT enterocolitica serotype 0:8: identification of the genes for mannose and
RT galactose biosynthesis and the gene for the O-antigen polymerase.";
RL Microbiology 142:277-288(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NCTC 13174 / 8081;
RX PubMed=17173484; DOI=10.1371/journal.pgen.0020206;
RA Thomson N.R., Howard S., Wren B.W., Holden M.T.G., Crossman L.,
RA Challis G.L., Churcher C., Mungall K., Brooks K., Chillingworth T.,
RA Feltwell T., Abdellah Z., Hauser H., Jagels K., Maddison M., Moule S.,
RA Sanders M., Whitehead S., Quail M.A., Dougan G., Parkhill J.,
RA Prentice M.B.;
RT "The complete genome sequence and comparative genome analysis of the high
RT pathogenicity Yersinia enterocolitica strain 8081.";
RL PLoS Genet. 2:2039-2051(2006).
CC -!- FUNCTION: Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-
CC deoxy-D-mannose. {ECO:0000255|HAMAP-Rule:MF_00955}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H2O;
CC Xref=Rhea:RHEA:23820, ChEBI:CHEBI:15377, ChEBI:CHEBI:57527,
CC ChEBI:CHEBI:57964; EC=4.2.1.47; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00955};
CC -!- COFACTOR:
CC Name=NADP(+); Xref=ChEBI:CHEBI:58349;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00955};
CC -!- PATHWAY: Bacterial outer membrane biogenesis; LPS O-antigen
CC biosynthesis. {ECO:0000269|PubMed:8932701}.
CC -!- PATHWAY: Nucleotide-sugar biosynthesis; GDP-L-fucose biosynthesis via
CC de novo pathway; GDP-L-fucose from GDP-alpha-D-mannose: step 1/2.
CC {ECO:0000269|PubMed:8932701}.
CC -!- SIMILARITY: Belongs to the NAD(P)-dependent epimerase/dehydratase
CC family. GDP-mannose 4,6-dehydratase subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_00955}.
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DR EMBL; U46859; AAC60773.1; -; Genomic_DNA.
DR EMBL; AM286415; CAL13110.1; -; Genomic_DNA.
DR RefSeq; WP_005167740.1; NC_008800.1.
DR RefSeq; YP_001007257.1; NC_008800.1.
DR AlphaFoldDB; Q56872; -.
DR SMR; Q56872; -.
DR STRING; 393305.YE3075; -.
DR EnsemblBacteria; CAL13110; CAL13110; YE3075.
DR KEGG; yen:YE3075; -.
DR PATRIC; fig|393305.7.peg.3272; -.
DR eggNOG; COG1089; Bacteria.
DR HOGENOM; CLU_007383_14_0_6; -.
DR OMA; TDCLYLG; -.
DR UniPathway; UPA00128; UER00190.
DR UniPathway; UPA00281; -.
DR Proteomes; UP000000642; Chromosome.
DR GO; GO:0008446; F:GDP-mannose 4,6-dehydratase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0070401; F:NADP+ binding; IEA:UniProtKB-UniRule.
DR GO; GO:0042351; P:'de novo' GDP-L-fucose biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0019673; P:GDP-mannose metabolic process; IEA:InterPro.
DR GO; GO:0009243; P:O antigen biosynthetic process; IEA:UniProtKB-UniPathway.
DR HAMAP; MF_00955; GDP_Man_dehydratase; 1.
DR InterPro; IPR006368; GDP_Man_deHydtase.
DR InterPro; IPR016040; NAD(P)-bd_dom.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR PANTHER; PTHR43715; PTHR43715; 1.
DR Pfam; PF16363; GDP_Man_Dehyd; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR01472; gmd; 1.
PE 3: Inferred from homology;
KW Lipopolysaccharide biosynthesis; Lyase; NADP.
FT CHAIN 1..372
FT /note="GDP-mannose 4,6-dehydratase"
FT /id="PRO_0000201719"
FT ACT_SITE 132
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT ACT_SITE 134
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT ACT_SITE 156
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT BINDING 8..13
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT BINDING 63..64
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT BINDING 85..89
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT BINDING 100
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT BINDING 160
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT BINDING 186
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT BINDING 191
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT CONFLICT 192..193
FT /note="GE -> PQ (in Ref. 1; AAC60773)"
FT /evidence="ECO:0000305"
FT CONFLICT 328
FT /note="E -> K (in Ref. 1; AAC60773)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 372 AA; 42122 MW; E5863EB5B5E584A1 CRC64;
MKKALITGIT GQDGSYLAEF LLEKGYQVHG IKRRSSSFNT SRIDHIYQDP HEVNPHFFLH
YGDLTDTSNL IRLVKEIQPD EIYNLGAQSH VAVSFESPEY TADVDAMGTL RLLEAVRING
LEHKTRFYQA STSELYGLVQ EIPQRETTPF YPRSPYAVAK MYAYWITVNY RESYGMYACN
GILFNHESPR RGETFVTRKI TRAIANIALG LEDCLYLGNM DSLRDWGHAK DYVRMQWMML
QQDQPEDFVI ATGKQITVRE FVRMSAKEAG IEIEFSGKGI DEIATISAIS DEYATSAKVG
DIIVRVDPRY FRPAEVETLL GDPSKAKEKL GWVPEITVEE MCAEMVAGDL QQAKQHALLK
ANGFDVSITL ES
