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P0AC88

- GM4D_ECOLI

UniProt

P0AC88 - GM4D_ECOLI

Protein

GDP-mannose 4,6-dehydratase

Gene

gmd

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 81 (01 Oct 2014)
      Sequence version 1 (08 Nov 2005)
      Previous versions | rss
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    Functioni

    Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose.1 PublicationUniRule annotation

    Catalytic activityi

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

    Cofactori

    NADP.2 PublicationsUniRule annotation

    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

    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: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11787. gmd.

    Subcellular locationi

    GO - Cellular componenti

    1. intracellular Source: InterPro

    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 – 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.
    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.
    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...
    MobiDBi 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

    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: October 1, 2014
    This is version 81 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