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P0AC88 (GM4D_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 70. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
GDP-mannose 4,6-dehydratase
EC=4.2.1.47
Alternative name(s):
GDP-D-mannose dehydratase
Gene names
Name:gmd
Synonyms:yefA, yefN
Ordered Locus Names:b2053, JW2038
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length373 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose. Ref.6

Catalytic activity

GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H2O. Ref.6

Cofactor

NADP. Ref.6 Ref.7

Pathway

Nucleotide-sugar biosynthesis; GDP-L-fucose biosynthesis via de novo pathway; GDP-L-fucose from GDP-alpha-D-mannose: step 1/2. Ref.6

Exopolysaccharide biosynthesis; colanic acid biosynthesis. Ref.6

Subunit structure

Homodimer. Ref.7

Sequence similarities

Belongs to the GDP-mannose 4,6-dehydratase family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 373373GDP-mannose 4,6-dehydratase HAMAP-Rule MF_00955
PRO_0000201712

Regions

Nucleotide binding9 – 146NADP By similarity
Nucleotide binding64 – 652NADP By similarity
Nucleotide binding86 – 905NADP By similarity

Sites

Active site1331
Active site1351Nucleophile
Active site1571Nucleophile
Binding site1011NADP By similarity
Binding site1611NADP Probable
Binding site1871NADP By similarity
Binding site1921NADP By similarity

Experimental info

Mutagenesis1331T → V: Strongly reduces activity. Ref.7
Mutagenesis1351E → Q: Strongly reduces activity.
Mutagenesis1571Y → F: Strongly reduces activity. Ref.7
Mutagenesis1611K → A: Strongly reduces activity. Ref.7

Secondary structure

1 ........................................................... 373
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0AC88 [UniParc].

Last modified November 8, 2005. Version 1.
Checksum: 1A9BA2A7C566DE11

FASTA37342,047
        10         20         30         40         50         60 
MSKVALITGV TGQDGSYLAE FLLEKGYEVH GIKRRASSFN TERVDHIYQD PHTCNPKFHL 

        70         80         90        100        110        120 
HYGDLSDTSN LTRILREVQP DEVYNLGAMS HVAVSFESPE YTADVDAMGT LRLLEAIRFL 

       130        140        150        160        170        180 
GLEKKTRFYQ ASTSELYGLV QEIPQKETTP FYPRSPYAVA KLYAYWITVN YRESYGMYAC 

       190        200        210        220        230        240 
NGILFNHESP RRGETFVTRK ITRAIANIAQ GLESCLYLGN MDSLRDWGHA KDYVKMQWMM 

       250        260        270        280        290        300 
LQQEQPEDFV IATGVQYSVR QFVEMAAAQL GIKLRFEGTG VEEKGIVVSV TGHDAPGVKP 

       310        320        330        340        350        360 
GDVIIAVDPR YFRPAEVETL LGDPTKAHEK LGWKPEITLR EMVSEMVAND LEAAKKHSLL 

       370 
KSHGYDVAIA LES

« Hide

References

« Hide 'large scale' references
[1]"Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid."
Stevenson G., Andrianopoulos K., Hobbs M., Reeves P.R.
J. Bacteriol. 178:4885-4893(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[2]"A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map."
Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S. expand/collapse author list , Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y., Horiuchi T.
DNA Res. 3:379-392(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[4]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]"Evidence for effect of random genetic drift on G+C content after lateral transfer of fucose pathway genes to Escherichia coli K-12."
Aoyama K., Haase A.M., Reeves P.R.
Mol. Biol. Evol. 11:829-838(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 50-373.
Strain: K12.
[6]"Expression, purification and characterization of GDP-D-mannose 4,6-dehydratase from Escherichia coli."
Sturla L., Bisso A., Zanardi D., Benatti U., de Flora A., Tonetti M.
FEBS Lett. 412:126-130(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, PATHWAY.
[7]"Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose."
Somoza J.R., Menon S., Schmidt H., Joseph-McCarthy D., Dessen A., Stahl M.L., Somers W.S., Sullivan F.X.
Structure 8:123-135(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS), COFACTOR, SUBUNIT, MUTAGENESIS OF THR-133; TYR-157 AND LYS-161.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		U38473 Genomic DNA. Translation: AAC77842.1.
U00096 Genomic DNA. Translation: AAC75114.1.
AP009048 Genomic DNA. Translation: BAA15909.1.
PIRD64971.
RefSeqNP_416557.1. NC_000913.2.
YP_490295.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1DB3X-ray2.30A2-373[»]
ProteinModelPortalP0AC88.
SMRP0AC88. Positions 2-358.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-48216N.
IntActP0AC88. 2 interactions.
STRING511145.b2053.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75114; AAC75114; b2053.
BAA15909; BAA15909; BAA15909.
GeneID12930696.
946562.
KEGGecj:Y75_p2016.
eco:b2053.
PATRIC32119439. VBIEscCol129921_2130.

Organism-specific databases

EchoBASEEB1735.
EcoGeneEG11787. gmd.

Phylogenomic databases

eggNOGCOG1089.
HOGENOMHOG000168003.
KOK01711.
OMAINPKYFR.
ProtClustDBCLSK880276.

Enzyme and pathway databases

BioCycEcoCyc:GDPMANDEHYDRA-MONOMER.
ECOL316407:JW2038-MONOMER.
MetaCyc:GDPMANDEHYDRA-MONOMER.
UniPathwayUPA00128; UER00190.
UPA00980.

Gene expression databases

GenevestigatorP0AC88.

Family and domain databases

Gene3D3.40.50.720. 1 hit.
HAMAPMF_00955. GDP_Man_dehydratase.
InterProIPR001509. Epimerase_deHydtase.
IPR006368. GDP_Man_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamPF01370. Epimerase. 1 hit.
[Graphical view]
TIGRFAMsTIGR01472. gmd. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP0AC88.

Entry information

Entry nameGM4D_ECOLI
AccessionPrimary (citable) accession number: P0AC88
Secondary accession number(s): P32054, P77687
Entry history
Integrated into UniProtKB/Swiss-Prot: November 8, 2005
Last sequence update: November 8, 2005
Last modified: May 29, 2013
This is version 70 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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