Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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: 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-HAMAP

GO - Biological processi

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 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. 186 interactors.
DIPiDIP-48216N.
IntActiP0AC88. 2 interactors.
STRINGi511145.b2053.

Structurei

Secondary structure

1373
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 8Combined sources5
Turni9 – 11Combined sources3
Helixi13 – 24Combined sources12
Beta strandi28 – 32Combined sources5
Beta strandi58 – 60Combined sources3
Helixi68 – 78Combined sources11
Beta strandi81 – 85Combined sources5
Turni91 – 96Combined sources6
Helixi99 – 106Combined sources8
Helixi108 – 119Combined sources12
Turni123 – 125Combined sources3
Beta strandi127 – 133Combined sources7
Helixi134 – 137Combined sources4
Beta strandi142 – 145Combined sources4
Helixi156 – 175Combined sources20
Beta strandi179 – 184Combined sources6
Helixi197 – 209Combined sources13
Beta strandi216 – 219Combined sources4
Helixi230 – 239Combined sources10
Beta strandi242 – 245Combined sources4
Beta strandi249 – 251Combined sources3
Helixi259 – 268Combined sources10
Turni269 – 271Combined sources3
Beta strandi272 – 278Combined sources7
Helixi280 – 282Combined sources3
Beta strandi284 – 290Combined sources7
Beta strandi292 – 294Combined sources3
Beta strandi303 – 307Combined sources5
Helixi309 – 311Combined sources3
Helixi325 – 331Combined sources7
Helixi339 – 355Combined sources17

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...

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.
OMAiDYQHRTG.
PhylomeDBiP0AC88.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00955. GDP_Man_dehydratase. 1 hit.
InterProiIPR006368. GDP_Man_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF16363. GDP_Man_Dehyd. 1 hit.
[Graphical view]
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.
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.
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. 186 interactors.
DIPiDIP-48216N.
IntActiP0AC88. 2 interactors.
STRINGi511145.b2053.

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.
PATRICi32119439. VBIEscCol129921_2130.

Organism-specific databases

EchoBASEiEB1735.
EcoGeneiEG11787. gmd.

Phylogenomic databases

eggNOGiENOG4105C0K. Bacteria.
COG1089. LUCA.
HOGENOMiHOG000168003.
InParanoidiP0AC88.
KOiK01711.
OMAiDYQHRTG.
PhylomeDBiP0AC88.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP0AC88.
PROiP0AC88.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00955. GDP_Man_dehydratase. 1 hit.
InterProiIPR006368. GDP_Man_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF16363. GDP_Man_Dehyd. 1 hit.
[Graphical view]
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 historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2005
Last sequence update: November 8, 2005
Last modified: November 2, 2016
This is version 96 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

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 one 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.