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P0AC88

- GM4D_ECOLI

UniProt

P0AC88 - GM4D_ECOLI

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Protein
GDP-mannose 4,6-dehydratase
Gene
gmd, yefA, yefN, b2053, JW2038
Organism
Escherichia coli (strain K12)
Status
Reviewed - 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.1 Publication

Catalytic activityi

GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H2O.1 Publication

Cofactori

NADP.2 Publications

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei101 – 1011NADP By similarity
Active sitei133 – 1331
Active sitei135 – 1351Nucleophile
Active sitei157 – 1571Nucleophile
Binding sitei161 – 1611NADP Inferred
Binding sitei187 – 1871NADP By similarity
Binding sitei192 – 1921NADP By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi9 – 146NADP By similarity
Nucleotide bindingi64 – 652NADP By similarity
Nucleotide bindingi86 – 905NADP By similarity

GO - Molecular functioni

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

GO - Biological processi

  1. 'de novo' GDP-L-fucose biosynthetic process Source: UniProtKB-UniPathway
  2. GDP-mannose metabolic process Source: InterPro
  3. colanic acid biosynthetic process Source: UniProtKB-UniPathway
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-dehydratase (EC:4.2.1.47)
Alternative name(s):
GDP-D-mannose dehydratase
Gene namesi
Name:gmd
Synonyms:yefA, yefN
Ordered Locus Names:b2053, JW2038
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG11787. gmd.

Subcellular locationi

GO - Cellular componenti

  1. intracellular Source: InterPro
Complete GO annotation...

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-dehydrataseUniRule annotation
PRO_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

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DB3X-ray2.30A2-373[»]
ProteinModelPortaliP0AC88.
SMRiP0AC88. Positions 2-358.

Miscellaneous databases

EvolutionaryTraceiP0AC88.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1089.
HOGENOMiHOG000168003.
KOiK01711.
OMAiARDYVKM.
OrthoDBiEOG6V7BNH.
PhylomeDBiP0AC88.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00955. GDP_Man_dehydratase.
InterProiIPR001509. Epimerase_deHydtase.
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

MSKVALITGV TGQDGSYLAE FLLEKGYEVH GIKRRASSFN TERVDHIYQD    50
PHTCNPKFHL HYGDLSDTSN LTRILREVQP DEVYNLGAMS HVAVSFESPE 100
YTADVDAMGT LRLLEAIRFL GLEKKTRFYQ ASTSELYGLV QEIPQKETTP 150
FYPRSPYAVA KLYAYWITVN YRESYGMYAC NGILFNHESP RRGETFVTRK 200
ITRAIANIAQ GLESCLYLGN MDSLRDWGHA KDYVKMQWMM LQQEQPEDFV 250
IATGVQYSVR QFVEMAAAQL GIKLRFEGTG VEEKGIVVSV TGHDAPGVKP 300
GDVIIAVDPR YFRPAEVETL LGDPTKAHEK LGWKPEITLR EMVSEMVAND 350
LEAAKKHSLL KSHGYDVAIA LES 373
Length:373
Mass (Da):42,047
Last modified:November 8, 2005 - v1
Checksum:i1A9BA2A7C566DE11
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
U38473 Genomic DNA. Translation: AAC77842.1 .
U00096 Genomic DNA. Translation: AAC75114.1 .
AP009048 Genomic DNA. Translation: BAA15909.1 .
PIRi D64971.
RefSeqi NP_416557.1. NC_000913.3.
YP_490295.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1DB3 X-ray 2.30 A 2-373 [» ]
ProteinModelPortali P0AC88.
SMRi P0AC88. Positions 2-358.
ModBasei Search...

Protein-protein interaction databases

DIPi DIP-48216N.
IntActi P0AC88. 2 interactions.
STRINGi 511145.b2053.

Proteomic databases

PRIDEi P0AC88.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC75114 ; AAC75114 ; b2053 .
BAA15909 ; BAA15909 ; BAA15909 .
GeneIDi 12930696.
946562.
KEGGi ecj:Y75_p2016.
eco:b2053.
PATRICi 32119439. VBIEscCol129921_2130.

Organism-specific databases

EchoBASEi EB1735.
EcoGenei EG11787. gmd.

Phylogenomic databases

eggNOGi COG1089.
HOGENOMi HOG000168003.
KOi K01711.
OMAi ARDYVKM.
OrthoDBi EOG6V7BNH.
PhylomeDBi P0AC88.

Enzyme and pathway databases

UniPathwayi UPA00128 ; UER00190 .
UPA00980 .
BioCyci EcoCyc:GDPMANDEHYDRA-MONOMER.
ECOL316407:JW2038-MONOMER.
MetaCyc:GDPMANDEHYDRA-MONOMER.
SABIO-RK P0AC88.

Miscellaneous databases

EvolutionaryTracei P0AC88.
PROi P0AC88.

Gene expression databases

Genevestigatori P0AC88.

Family and domain databases

Gene3Di 3.40.50.720. 1 hit.
HAMAPi MF_00955. GDP_Man_dehydratase.
InterProi IPR001509. Epimerase_deHydtase.
IPR006368. GDP_Man_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view ]
Pfami PF01370. Epimerase. 1 hit.
[Graphical view ]
TIGRFAMsi TIGR01472. gmd. 1 hit.
ProtoNeti Search...

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(1996) [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(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.

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: May 14, 2014
This is version 80 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

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