Reviewed, UniProtKB/Swiss-Prot Q56598 (GM4D2_VIBCH)

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

Gene names

Name:	rfbD
Synonyms:	gmd

Organism

Vibrio cholerae

Taxonomic identifier

666 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio

Protein attributes

Sequence length	372 AA.
Sequence status	Complete.
Protein existence	Inferred from homology.

General annotation (Comments)

Catalytic activity	GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H2O.
Cofactor	NAD.
Pathway	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
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_0000201718
Sites
	Active site	133	1	By similarity
	Active site	135	1	Nucleophile By similarity
	Active site	157	1	Nucleophile By similarity
	Binding site	161	1	NADP By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q56598-1 [UniParc]. Last modified July 15, 1999. Version 2. Checksum: 11762663764B3E57	FASTA	372	41,992
	10 20 30 40 50 60 MKKKALITGV TGQDGSYLAE FLLAKGYEVH GIKRRASSFN TQRVDHIYQD PHVDNASFIL 70 80 90 100 110 120 HYGDLTDSSN LTRILQEVKP DEVYNLGAQS HVAVSFESPE YTADVDAMGT LRLLEAIRLL 130 140 150 160 170 180 GLEKTTKFYQ ASTSELYGLV QETPQKETTP FYPRSPYAVA KMYAYWIVVN YRESYGMYAC 190 200 210 220 230 240 NGILFNHESP RRGETFVTRK ITRGLANIAQ GLEKCLYMGN MDALRDWGHA KDYVRMQWMM 250 260 270 280 290 300 LQQDQPEDFV IATGVQYSVR QFIEWSAKEL GVTLTFEGQG VDEKGIVTAI EGDKAPALKV 310 320 330 340 350 360 GDVVVQIDPR YFRPAEVETL LGDPSKAKQK LGWTPEITVQ EMCAEMVMED LKVAQRHALL 370 KLHGHDVPVS VE

References

[1]	"Novel Vibrio cholerae O139 genes involved in lipopolysaccharide biosynthesis." Stroeher U.H., Parasivam G., Dredge B.K., Manning P.A. J. Bacteriol. 179:2740-2747(1997) [PubMed: 9098074] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: AI-1837 / Serotype O139.
[2]	"The genes responsible for O-antigen synthesis of Vibrio cholerae O139 are closely related to those of Vibrio cholerae O22." Yamasaki S., Shimizu T., Hoshino K., Ho S.-T., Shimada T., Nair G.B., Takeda Y. Gene 237:321-332(1999) [PubMed: 10521656] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 51394 / MO45 / Serotype O139.
[3]	Dumontier S.E., Escuyer V.E., Berche P. Submitted (OCT-1995) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-348. Strain: ATCC 51394 / MO45 / Serotype O139.

Cross-references

Sequence databases
EMBL GenBank DDBJ	Y07786 Genomic DNA. Translation: CAA69111.1. AB012956 Genomic DNA. Translation: BAA33595.1. U24571 Genomic DNA. Translation: AAA77032.1.
3D structure databases
SMR	Q56598. Positions 3-358.
ModBase	Search...
Enzyme and pathway databases
BRENDA	4.2.1.47. 19019.
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

GM4D2_VIBCH

Accession

Primary (citable) accession number: Q56598

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	July 15, 1999
Last modified:	February 9, 2010
This is version 54 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)