Reviewed, UniProtKB/Swiss-Prot Q56872 (GM4D_YERE8)

Names and origin

Protein names

Recommended name:
    Probable GDP-mannose 4,6-dehydratase
    EC=4.2.1.47
Alternative name(s):
    GDP-D-mannose dehydratase
    ORF13.7

Gene names

Name:	gmd
Ordered Locus Names:	YE3075

Organism

Yersinia enterocolitica serotype O:8 / biotype 1B (strain 8081) [Complete proteome] [HAMAP]

Taxonomic identifier

393305 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Yersinia

Protein attributes

Sequence length	372 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred from homology.

General annotation (Comments)

Catalytic activity	GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H2O.
Cofactor	NAD.
Pathway	Bacterial outer membrane biogenesis; LPS O-antigen biosynthesis. Nucleotide-sugar biosynthesis; GDP-L-fucose biosynthesis via de novo pathway; GDP-L-fucose from GDP-alpha-D-mannose: step 1/2.
Sequence similarities	Belongs to the GDP-mannose 4,6-dehydratase family.

Ontologies

Keywords
Biological process	Lipopolysaccharide biosynthesis
Ligand	NAD
Molecular function	Lyase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	GDP-mannose metabolic process Inferred from electronic annotation. Source: InterPro lipopolysaccharide biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	intracellular Inferred from electronic annotation. Source: InterPro
Molecular function	GDP-mannose 4,6-dehydratase activity Inferred from electronic annotation. Source: EC coenzyme binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 372	372	Probable GDP-mannose 4,6-dehydratase		PRO_0000201719
Sites
	Active site	132	1	By similarity
	Active site	134	1	Nucleophile By similarity
	Active site	156	1	Nucleophile By similarity
	Binding site	160	1	NADP By similarity
Experimental info
	Sequence conflict	192 – 193	2	GE → PQ in AAC60773. Ref.1
	Sequence conflict	328	1	E → K in AAC60773. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q56872-1 [UniParc]. Last modified March 20, 2007. Version 2. Checksum: E5863EB5B5E584A1	FASTA	372	42,122
	10 20 30 40 50 60 MKKALITGIT GQDGSYLAEF LLEKGYQVHG IKRRSSSFNT SRIDHIYQDP HEVNPHFFLH 70 80 90 100 110 120 YGDLTDTSNL IRLVKEIQPD EIYNLGAQSH VAVSFESPEY TADVDAMGTL RLLEAVRING 130 140 150 160 170 180 LEHKTRFYQA STSELYGLVQ EIPQRETTPF YPRSPYAVAK MYAYWITVNY RESYGMYACN 190 200 210 220 230 240 GILFNHESPR RGETFVTRKI TRAIANIALG LEDCLYLGNM DSLRDWGHAK DYVRMQWMML 250 260 270 280 290 300 QQDQPEDFVI ATGKQITVRE FVRMSAKEAG IEIEFSGKGI DEIATISAIS DEYATSAKVG 310 320 330 340 350 360 DIIVRVDPRY FRPAEVETLL GDPSKAKEKL GWVPEITVEE MCAEMVAGDL QQAKQHALLK 370 ANGFDVSITL ES

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The gene cluster directing O-antigen biosynthesis in Yersinia enterocolitica serotype 0:8: identification of the genes for mannose and galactose biosynthesis and the gene for the O-antigen polymerase." Zhang L., Toivanen P., Skurnik M. Microbiology 142:277-288(1996) [PubMed: 8932701] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081." Thomson N.R., Howard S., Wren B.W., Holden M.T.G., Crossman L., Challis G.L., Churcher C., Mungall K., Brooks K., Chillingworth T., Feltwell T., Abdellah Z., Hauser H., Jagels K., Maddison M., Moule S., Sanders M., Whitehead S. , Quail M.A., Dougan G., Parkhill J., Prentice M.B. PLoS Genet. 2:2039-2051(2006) [PubMed: 17173484] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	U46859 Genomic DNA. Translation: AAC60773.1. AM286415 Genomic DNA. Translation: CAL13110.1.
RefSeq	YP_001007257.1.
3D structure databases
HSSP	HSSP built from PDB template 1DB3 based on UniProtKB P32054.
ModBase	Search...
Protein-protein interaction databases
STRING	Q56872.
Genome annotation databases
GeneID	4714562.
GenomeReviews	Gene locus YE3075 in contig AM286415_GR.
KEGG	yen:YE3075.
NMPDR	fig|630.2.peg.3007.
Organism-specific databases
CMR	Search...
Phylogenomic databases
OMA	LANISQG.
Family and domain databases
InterPro	IPR001509. Epimerase_deHydtase. IPR006368. GDP_Man_deHydtase. IPR016040. NAD(P)-bd_dom. [Graphical view]
Gene3D	G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.
PANTHER	PTHR10366:SF32. GDP_mann_dehyd. 1 hit.
Pfam	PF01370. Epimerase. 1 hit. [Graphical view]
TIGRFAMs	TIGR01472. gmd. 1 hit.
ProtoNet	Search...

Entry information

Entry name

GM4D_YERE8

Accession

Primary (citable) accession number: Q56872
Secondary accession number(s): A1JN62

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	March 20, 2007
Last modified:	November 3, 2009
This is version 57 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)