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O60547

- GMDS_HUMAN

UniProt

O60547 - GMDS_HUMAN

Protein

GDP-mannose 4,6 dehydratase

Gene

GMDS

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 132 (01 Oct 2014)
      Sequence version 1 (01 Aug 1998)
      Previous versions | rss
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    Functioni

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

    Catalytic activityi

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

    Cofactori

    NADP.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei123 – 1231NADP1 Publication
    Active sitei155 – 1551By similarity
    Active sitei157 – 1571NucleophileBy similarity
    Active sitei179 – 1791NucleophileBy similarity
    Binding sitei183 – 1831NADP1 Publication
    Binding sitei209 – 2091NADP1 Publication
    Binding sitei214 – 2141NADP1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi30 – 356NADP1 Publication
    Nucleotide bindingi55 – 584NADP1 Publication
    Nucleotide bindingi86 – 872NADP1 Publication
    Nucleotide bindingi108 – 1125NADP1 Publication

    GO - Molecular functioni

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

    GO - Biological processi

    1. 'de novo' GDP-L-fucose biosynthetic process Source: UniProtKB
    2. GDP-mannose metabolic process Source: UniProtKB
    3. Notch signaling pathway Source: UniProtKB

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    NADP

    Enzyme and pathway databases

    UniPathwayiUPA00128; UER00190.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    GDP-mannose 4,6 dehydratase (EC:4.2.1.47)
    Alternative name(s):
    GDP-D-mannose dehydratase
    Short name:
    GMD
    Gene namesi
    Name:GMDS
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 6

    Organism-specific databases

    HGNCiHGNC:4369. GMDS.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB
    2. extracellular vesicular exosome Source: UniProt

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA28754.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 372371GDP-mannose 4,6 dehydratasePRO_0000201705Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylalanine1 Publication

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiO60547.
    PaxDbiO60547.
    PeptideAtlasiO60547.
    PRIDEiO60547.

    PTM databases

    PhosphoSiteiO60547.

    Expressioni

    Gene expression databases

    ArrayExpressiO60547.
    BgeeiO60547.
    CleanExiHS_GMDS.
    GenevestigatoriO60547.

    Organism-specific databases

    HPAiHPA031528.

    Interactioni

    Protein-protein interaction databases

    BioGridi109024. 12 interactions.
    IntActiO60547. 1 interaction.
    STRINGi9606.ENSP00000370194.

    Structurei

    Secondary structure

    1
    372
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi25 – 295
    Turni30 – 323
    Helixi34 – 4512
    Beta strandi49 – 546
    Turni63 – 653
    Helixi66 – 683
    Beta strandi80 – 845
    Helixi90 – 10011
    Beta strandi103 – 1075
    Helixi114 – 1196
    Helixi121 – 1288
    Helixi130 – 14112
    Turni145 – 1473
    Beta strandi149 – 1557
    Helixi156 – 1583
    Beta strandi163 – 1675
    Helixi178 – 19720
    Beta strandi200 – 2067
    Helixi219 – 23113
    Beta strandi238 – 2414
    Helixi252 – 26413
    Beta strandi265 – 2673
    Beta strandi271 – 2733
    Helixi281 – 29111
    Beta strandi296 – 3005
    Helixi302 – 3043
    Beta strandi306 – 3094
    Turni310 – 3123
    Beta strandi315 – 3195
    Helixi321 – 3233
    Helixi337 – 3437
    Helixi351 – 36818

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1T2AX-ray1.84A/B/C/D23-372[»]
    ProteinModelPortaliO60547.
    SMRiO60547. Positions 23-369.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO60547.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG1089.
    HOGENOMiHOG000168003.
    HOVERGENiHBG000727.
    InParanoidiO60547.
    KOiK01711.
    OMAiFMHIGKT.
    OrthoDBiEOG7K6PV5.
    PhylomeDBiO60547.
    TreeFamiTF300682.

    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.

    Sequences (2)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: O60547-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MAHAPARCPS ARGSGDGEMG KPRNVALITG ITGQDGSYLA EFLLEKGYEV    50
    HGIVRRSSSF NTGRIEHLYK NPQAHIEGNM KLHYGDLTDS TCLVKIINEV 100
    KPTEIYNLGA QSHVKISFDL AEYTADVDGV GTLRLLDAVK TCGLINSVKF 150
    YQASTSELYG KVQEIPQKET TPFYPRSPYG AAKLYAYWIV VNFREAYNLF 200
    AVNGILFNHE SPRRGANFVT RKISRSVAKI YLGQLECFSL GNLDAKRDWG 250
    HAKDYVEAMW LMLQNDEPED FVIATGEVHS VREFVEKSFL HIGKTIVWEG 300
    KNENEVGRCK ETGKVHVTVD LKYYRPTEVD FLQGDCTKAK QKLNWKPRVA 350
    FDELVREMVH ADVELMRTNP NA 372
    Length:372
    Mass (Da):41,950
    Last modified:August 1, 1998 - v1
    Checksum:iB1BAC441736D4C2B
    GO
    Isoform 2 (identifier: O60547-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-34: MAHAPARCPSARGSGDGEMGKPRNVALITGITGQ → MCKM

    Note: No experimental confirmation available.

    Show »
    Length:342
    Mass (Da):39,054
    Checksum:iED43224234CC0A7B
    GO

    Sequence cautioni

    The sequence AAC24501.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti156 – 1561S → N in CAG46745. 1 PublicationCurated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 3434MAHAP…GITGQ → MCKM in isoform 2. 1 PublicationVSP_047324Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF042377 mRNA. Translation: AAC13553.1.
    AF040260 mRNA. Translation: AAC24501.1. Different initiation.
    CR541929 mRNA. Translation: CAG46727.1.
    CR541947 mRNA. Translation: CAG46745.1.
    AL033517 Genomic DNA. No translation available.
    AL034344 Genomic DNA. No translation available.
    AL035693 Genomic DNA. No translation available.
    AL137179 Genomic DNA. No translation available.
    AL158139 Genomic DNA. No translation available.
    AL354670 Genomic DNA. No translation available.
    AL451141 Genomic DNA. No translation available.
    AL591048 Genomic DNA. No translation available.
    BC000117 mRNA. Translation: AAH00117.1.
    CCDSiCCDS4474.1. [O60547-1]
    CCDS58994.1. [O60547-2]
    RefSeqiNP_001240775.1. NM_001253846.1. [O60547-2]
    NP_001491.1. NM_001500.3. [O60547-1]
    UniGeneiHs.144496.
    Hs.660919.

    Genome annotation databases

    EnsembliENST00000380815; ENSP00000370194; ENSG00000112699. [O60547-1]
    ENST00000530927; ENSP00000436726; ENSG00000112699. [O60547-2]
    GeneIDi2762.
    KEGGihsa:2762.
    UCSCiuc003mtq.3. human. [O60547-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF042377 mRNA. Translation: AAC13553.1 .
    AF040260 mRNA. Translation: AAC24501.1 . Different initiation.
    CR541929 mRNA. Translation: CAG46727.1 .
    CR541947 mRNA. Translation: CAG46745.1 .
    AL033517 Genomic DNA. No translation available.
    AL034344 Genomic DNA. No translation available.
    AL035693 Genomic DNA. No translation available.
    AL137179 Genomic DNA. No translation available.
    AL158139 Genomic DNA. No translation available.
    AL354670 Genomic DNA. No translation available.
    AL451141 Genomic DNA. No translation available.
    AL591048 Genomic DNA. No translation available.
    BC000117 mRNA. Translation: AAH00117.1 .
    CCDSi CCDS4474.1. [O60547-1 ]
    CCDS58994.1. [O60547-2 ]
    RefSeqi NP_001240775.1. NM_001253846.1. [O60547-2 ]
    NP_001491.1. NM_001500.3. [O60547-1 ]
    UniGenei Hs.144496.
    Hs.660919.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1T2A X-ray 1.84 A/B/C/D 23-372 [» ]
    ProteinModelPortali O60547.
    SMRi O60547. Positions 23-369.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 109024. 12 interactions.
    IntActi O60547. 1 interaction.
    STRINGi 9606.ENSP00000370194.

    PTM databases

    PhosphoSitei O60547.

    Proteomic databases

    MaxQBi O60547.
    PaxDbi O60547.
    PeptideAtlasi O60547.
    PRIDEi O60547.

    Protocols and materials databases

    DNASUi 2762.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000380815 ; ENSP00000370194 ; ENSG00000112699 . [O60547-1 ]
    ENST00000530927 ; ENSP00000436726 ; ENSG00000112699 . [O60547-2 ]
    GeneIDi 2762.
    KEGGi hsa:2762.
    UCSCi uc003mtq.3. human. [O60547-1 ]

    Organism-specific databases

    CTDi 2762.
    GeneCardsi GC06M001624.
    HGNCi HGNC:4369. GMDS.
    HPAi HPA031528.
    MIMi 602884. gene.
    neXtProti NX_O60547.
    PharmGKBi PA28754.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG1089.
    HOGENOMi HOG000168003.
    HOVERGENi HBG000727.
    InParanoidi O60547.
    KOi K01711.
    OMAi FMHIGKT.
    OrthoDBi EOG7K6PV5.
    PhylomeDBi O60547.
    TreeFami TF300682.

    Enzyme and pathway databases

    UniPathwayi UPA00128 ; UER00190 .

    Miscellaneous databases

    ChiTaRSi GMDS. human.
    EvolutionaryTracei O60547.
    GeneWikii GMDS_(gene).
    GenomeRNAii 2762.
    NextBioi 10866.
    PROi O60547.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi O60547.
    Bgeei O60547.
    CleanExi HS_GMDS.
    Genevestigatori O60547.

    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. "Molecular cloning of human GDP-mannose 4,6-dehydratase and reconstitution of GDP-fucose biosynthesis in vitro."
      Sullivan F.X., Kumar R., Kriz R., Stahl M., Xu G.-Y., Rouse J., Chang X.J., Boodhoo A., Potvin B., Cumming D.A.
      J. Biol. Chem. 273:8193-8202(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    2. "Molecular cloning and expression of GDP-D-mannose-4,6-dehydratase, a key enzyme for fucose metabolism defective in Lec13 cells."
      Ohyama C., Smith P.L., Angata K., Fukuda M.N., Lowe J.B., Fukuda M.
      J. Biol. Chem. 273:14582-14587(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
      Tissue: Brain.
    3. "Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
      Halleck A., Ebert L., Mkoundinya M., Schick M., Eisenstein S., Neubert P., Kstrang K., Schatten R., Shen B., Henze S., Mar W., Korn B., Zuo D., Hu Y., LaBaer J.
      Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    4. "The DNA sequence and analysis of human chromosome 6."
      Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
      , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
      Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Eye.
    6. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
      Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
      Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
    7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. "Crystal structure and biophysical characterization of human GDP-D-mannose 4,6-dehydratase."
      Vedadi M., Walker J.R., Sharma S., Houston S., Wasney G., Loppnau P., Oppermann U.
      Submitted (APR-2004) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS) OF 23-372 IN COMPLEX WITH NADP, COFACTOR.

    Entry informationi

    Entry nameiGMDS_HUMAN
    AccessioniPrimary (citable) accession number: O60547
    Secondary accession number(s): E9PI88
    , O75357, Q5T954, Q6FH09, Q9UGZ3, Q9UJK9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 2000
    Last sequence update: August 1, 1998
    Last modified: October 1, 2014
    This is version 132 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 6
      Human chromosome 6: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    4. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    5. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3