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Protein

GDP-mannose 4,6-dehydratase

Gene

gmd

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose.UniRule annotation1 Publication

Catalytic activityi

GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H2O.UniRule annotation1 Publication

Cofactori

NADP(+)UniRule annotation2 Publications

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei101 – 1011NADPUniRule annotation
Active sitei133 – 1331
Active sitei135 – 1351Nucleophile
Active sitei157 – 1571Nucleophile
Binding sitei161 – 1611NADPCurated
Binding sitei187 – 1871NADPUniRule annotation
Binding sitei192 – 1921NADPUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi9 – 146NADPUniRule annotation
Nucleotide bindingi64 – 652NADPUniRule annotation
Nucleotide bindingi86 – 905NADPUniRule annotation

GO - Molecular functioni

  1. GDP-mannose 4,6-dehydratase activity Source: EcoCyc
  2. NADP+ binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. 'de novo' GDP-L-fucose biosynthetic process Source: UniProtKB-UniPathway
  2. colanic acid biosynthetic process Source: UniProtKB-UniPathway
  3. GDP-mannose metabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

NADP

Enzyme and pathway databases

BioCyciEcoCyc:GDPMANDEHYDRA-MONOMER.
ECOL316407:JW2038-MONOMER.
MetaCyc:GDPMANDEHYDRA-MONOMER.
SABIO-RKP0AC88.
UniPathwayiUPA00128; UER00190.
UPA00980.

Names & Taxonomyi

Protein namesi
Recommended name:
GDP-mannose 4,6-dehydrataseUniRule annotation (EC:4.2.1.47UniRule annotation)
Alternative name(s):
GDP-D-mannose dehydrataseUniRule annotation
Gene namesi
Name:gmdUniRule annotation
Synonyms:yefA, yefN
Ordered Locus Names:b2053, JW2038
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11787. gmd.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi133 – 1331T → V: Strongly reduces activity. 1 Publication
Mutagenesisi135 – 1351E → Q: Strongly reduces activity.
Mutagenesisi157 – 1571Y → F: Strongly reduces activity. 1 Publication
Mutagenesisi161 – 1611K → A: Strongly reduces activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 373373GDP-mannose 4,6-dehydratasePRO_0000201712Add
BLAST

Proteomic databases

PRIDEiP0AC88.

Expressioni

Gene expression databases

GenevestigatoriP0AC88.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

DIPiDIP-48216N.
IntActiP0AC88. 2 interactions.
STRINGi511145.b2053.

Structurei

Secondary structure

1
373
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 85Combined sources
Turni9 – 113Combined sources
Helixi13 – 2412Combined sources
Beta strandi28 – 325Combined sources
Beta strandi58 – 603Combined sources
Helixi68 – 7811Combined sources
Beta strandi81 – 855Combined sources
Turni91 – 966Combined sources
Helixi99 – 1068Combined sources
Helixi108 – 11912Combined sources
Turni123 – 1253Combined sources
Beta strandi127 – 1337Combined sources
Helixi134 – 1374Combined sources
Beta strandi142 – 1454Combined sources
Helixi156 – 17520Combined sources
Beta strandi179 – 1846Combined sources
Helixi197 – 20913Combined sources
Beta strandi216 – 2194Combined sources
Helixi230 – 23910Combined sources
Beta strandi242 – 2454Combined sources
Beta strandi249 – 2513Combined sources
Helixi259 – 26810Combined sources
Turni269 – 2713Combined sources
Beta strandi272 – 2787Combined sources
Helixi280 – 2823Combined sources
Beta strandi284 – 2907Combined sources
Beta strandi292 – 2943Combined sources
Beta strandi303 – 3075Combined sources
Helixi309 – 3113Combined sources
Helixi325 – 3317Combined sources
Helixi339 – 35517Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DB3X-ray2.30A2-373[»]
ProteinModelPortaliP0AC88.
SMRiP0AC88. Positions 2-358.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AC88.

Family & Domainsi

Sequence similaritiesi

Belongs to the NAD(P)-dependent epimerase/dehydratase family. GDP-mannose 4,6-dehydratase subfamily.UniRule annotation

Phylogenomic databases

eggNOGiCOG1089.
HOGENOMiHOG000168003.
InParanoidiP0AC88.
KOiK01711.
OMAiTDCLYLG.
OrthoDBiEOG6V7BNH.
PhylomeDBiP0AC88.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00955. GDP_Man_dehydratase.
InterProiIPR001509. Epimerase_deHydtase_N.
IPR006368. GDP_Man_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF01370. Epimerase. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01472. gmd. 1 hit.

Sequencei

Sequence statusi: Complete.

P0AC88-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKVALITGV TGQDGSYLAE FLLEKGYEVH GIKRRASSFN TERVDHIYQD
60 70 80 90 100
PHTCNPKFHL HYGDLSDTSN LTRILREVQP DEVYNLGAMS HVAVSFESPE
110 120 130 140 150
YTADVDAMGT LRLLEAIRFL GLEKKTRFYQ ASTSELYGLV QEIPQKETTP
160 170 180 190 200
FYPRSPYAVA KLYAYWITVN YRESYGMYAC NGILFNHESP RRGETFVTRK
210 220 230 240 250
ITRAIANIAQ GLESCLYLGN MDSLRDWGHA KDYVKMQWMM LQQEQPEDFV
260 270 280 290 300
IATGVQYSVR QFVEMAAAQL GIKLRFEGTG VEEKGIVVSV TGHDAPGVKP
310 320 330 340 350
GDVIIAVDPR YFRPAEVETL LGDPTKAHEK LGWKPEITLR EMVSEMVAND
360 370
LEAAKKHSLL KSHGYDVAIA LES
Length:373
Mass (Da):42,047
Last modified:November 8, 2005 - v1
Checksum:i1A9BA2A7C566DE11
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U38473 Genomic DNA. Translation: AAC77842.1.
U00096 Genomic DNA. Translation: AAC75114.1.
AP009048 Genomic DNA. Translation: BAA15909.1.
PIRiD64971.
RefSeqiNP_416557.1. NC_000913.3.
YP_490295.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC75114; AAC75114; b2053.
BAA15909; BAA15909; BAA15909.
GeneIDi12930696.
946562.
KEGGiecj:Y75_p2016.
eco:b2053.
PATRICi32119439. VBIEscCol129921_2130.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U38473 Genomic DNA. Translation: AAC77842.1.
U00096 Genomic DNA. Translation: AAC75114.1.
AP009048 Genomic DNA. Translation: BAA15909.1.
PIRiD64971.
RefSeqiNP_416557.1. NC_000913.3.
YP_490295.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DB3X-ray2.30A2-373[»]
ProteinModelPortaliP0AC88.
SMRiP0AC88. Positions 2-358.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48216N.
IntActiP0AC88. 2 interactions.
STRINGi511145.b2053.

Proteomic databases

PRIDEiP0AC88.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75114; AAC75114; b2053.
BAA15909; BAA15909; BAA15909.
GeneIDi12930696.
946562.
KEGGiecj:Y75_p2016.
eco:b2053.
PATRICi32119439. VBIEscCol129921_2130.

Organism-specific databases

EchoBASEiEB1735.
EcoGeneiEG11787. gmd.

Phylogenomic databases

eggNOGiCOG1089.
HOGENOMiHOG000168003.
InParanoidiP0AC88.
KOiK01711.
OMAiTDCLYLG.
OrthoDBiEOG6V7BNH.
PhylomeDBiP0AC88.

Enzyme and pathway databases

UniPathwayiUPA00128; UER00190.
UPA00980.
BioCyciEcoCyc:GDPMANDEHYDRA-MONOMER.
ECOL316407:JW2038-MONOMER.
MetaCyc:GDPMANDEHYDRA-MONOMER.
SABIO-RKP0AC88.

Miscellaneous databases

EvolutionaryTraceiP0AC88.
PROiP0AC88.

Gene expression databases

GenevestigatoriP0AC88.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00955. GDP_Man_dehydratase.
InterProiIPR001509. Epimerase_deHydtase_N.
IPR006368. GDP_Man_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF01370. Epimerase. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01472. gmd. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. 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(2005) [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(1993) [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(1996) [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(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS), COFACTOR, SUBUNIT, MUTAGENESIS OF THR-133; TYR-157 AND LYS-161.

Entry informationi

Entry nameiGM4D_ECOLI
AccessioniPrimary (citable) accession number: P0AC88
Secondary accession number(s): P32054, P77687
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2005
Last sequence update: November 8, 2005
Last modified: January 7, 2015
This is version 84 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.