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Protein

GDP-mannose 4,6-dehydratase

Gene

gmd

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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: GDP-L-fucose biosynthesis via de novo pathway

This protein is involved in step 1 of the subpathway that synthesizes GDP-L-fucose from GDP-alpha-D-mannose.1 Publication
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. GDP-mannose 4,6-dehydratase (gmd)
  2. GDP-L-fucose synthase (fcl)
This subpathway is part of the pathway GDP-L-fucose biosynthesis via de novo pathway, which is itself part of Nucleotide-sugar biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes GDP-L-fucose from GDP-alpha-D-mannose, the pathway GDP-L-fucose biosynthesis via de novo pathway and in Nucleotide-sugar biosynthesis.

Pathwayi: colanic acid biosynthesis

This protein is involved in the pathway colanic acid biosynthesis, which is part of Exopolysaccharide biosynthesis.1 Publication
View all proteins of this organism that are known to be involved in the pathway colanic acid biosynthesis and in Exopolysaccharide biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei101NADPUniRule annotation1
Active sitei1331 Publication1
Active sitei135Nucleophile1 Publication1
Active sitei157Nucleophile1 Publication1
Binding sitei161NADPCurated1
Binding sitei187NADPUniRule annotation1
Binding sitei192NADPUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi9 – 14NADPUniRule annotation6
Nucleotide bindingi64 – 65NADPUniRule annotation2
Nucleotide bindingi86 – 90NADPUniRule annotation5

GO - Molecular functioni

  • GDP-mannose 4,6-dehydratase activity Source: EcoCyc
  • NADP+ binding Source: UniProtKB-UniRule

GO - Biological processi

Keywordsi

Molecular functionLyase
LigandNADP

Enzyme and pathway databases

BioCyciEcoCyc:GDPMANDEHYDRA-MONOMER
MetaCyc:GDPMANDEHYDRA-MONOMER
SABIO-RKiP0AC88
UniPathwayi
UPA00128;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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11787 gmd

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi133T → V: Strongly reduces activity. 1 Publication1
Mutagenesisi135E → Q: Strongly reduces activity. 1 Publication1
Mutagenesisi157Y → F: Strongly reduces activity. 1 Publication1
Mutagenesisi161K → A: Strongly reduces activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002017121 – 373GDP-mannose 4,6-dehydrataseAdd BLAST373

Proteomic databases

PaxDbiP0AC88
PRIDEiP0AC88

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi4259690, 193 interactors
DIPiDIP-48216N
IntActiP0AC88, 2 interactors
STRINGi316385.ECDH10B_2203

Structurei

Secondary structure

1373
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP0AC88
SMRiP0AC88
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

eggNOGiENOG4105C0K Bacteria
COG1089 LUCA
HOGENOMiHOG000168003
InParanoidiP0AC88
KOiK01711
OMAiTDCLYLG
PhylomeDBiP0AC88

Family and domain databases

HAMAPiMF_00955 GDP_Man_dehydratase, 1 hit
InterProiView protein in InterPro
IPR006368 GDP_Man_deHydtase
IPR016040 NAD(P)-bd_dom
IPR036291 NAD(P)-bd_dom_sf
PANTHERiPTHR43715 PTHR43715, 1 hit
PfamiView protein in Pfam
PF16363 GDP_Man_Dehyd, 1 hit
SUPFAMiSSF51735 SSF51735, 1 hit
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
WP_000048190.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC75114; AAC75114; b2053
BAA15909; BAA15909; BAA15909
GeneIDi946562
KEGGiecj:JW2038
eco:b2053
PATRICifig|1411691.4.peg.198

Similar proteinsi

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
WP_000048190.1, NZ_LN832404.1

3D structure databases

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

Protein-protein interaction databases

BioGridi4259690, 193 interactors
DIPiDIP-48216N
IntActiP0AC88, 2 interactors
STRINGi316385.ECDH10B_2203

Proteomic databases

PaxDbiP0AC88
PRIDEiP0AC88

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75114; AAC75114; b2053
BAA15909; BAA15909; BAA15909
GeneIDi946562
KEGGiecj:JW2038
eco:b2053
PATRICifig|1411691.4.peg.198

Organism-specific databases

EchoBASEiEB1735
EcoGeneiEG11787 gmd

Phylogenomic databases

eggNOGiENOG4105C0K Bacteria
COG1089 LUCA
HOGENOMiHOG000168003
InParanoidiP0AC88
KOiK01711
OMAiTDCLYLG
PhylomeDBiP0AC88

Enzyme and pathway databases

UniPathwayi
UPA00128;UER00190

UPA00980

BioCyciEcoCyc:GDPMANDEHYDRA-MONOMER
MetaCyc:GDPMANDEHYDRA-MONOMER
SABIO-RKiP0AC88

Miscellaneous databases

EvolutionaryTraceiP0AC88
PROiPR:P0AC88

Family and domain databases

HAMAPiMF_00955 GDP_Man_dehydratase, 1 hit
InterProiView protein in InterPro
IPR006368 GDP_Man_deHydtase
IPR016040 NAD(P)-bd_dom
IPR036291 NAD(P)-bd_dom_sf
PANTHERiPTHR43715 PTHR43715, 1 hit
PfamiView protein in Pfam
PF16363 GDP_Man_Dehyd, 1 hit
SUPFAMiSSF51735 SSF51735, 1 hit
TIGRFAMsiTIGR01472 gmd, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiGM4D_ECOLI
AccessioniPrimary (citable) accession number: P0AC88
Secondary accession number(s): P32054, P77687
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 8, 2005
Last sequence update: November 8, 2005
Last modified: October 10, 2018
This is version 106 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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