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Protein

GDP-mannose 3,5-epimerase 1

Gene

GME-1

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes a reversible epimerization of GDP-D-mannose that precedes the committed step in the biosynthesis of vitamin C (L-ascorbate), resulting in the hydrolysis of the highly energetic glycosyl-pyrophosphoryl linkage. Able to catalyze 2 distinct epimerization reactions and can release both GDP-L-galactose and GDP-L-gulose from GDP-mannose.1 Publication

Catalytic activityi

GDP-alpha-D-mannose = GDP-beta-L-galactose.

Cofactori

NAD+Curated

Enzyme regulationi

Strongly activated by NAD. Activated by NADP. Slightly activated by NADH and NADPH. Inhibited by GDP.1 Publication

Kineticsi

The catalytic efficiency increases by 2-fold in the presence of NAD+.
  1. KM=7.12 µM for GDP-mannose1 Publication
  2. KM=12 µM for GDP-mannose (in the presence of 20 µM NAD+)1 Publication

    pH dependencei

    Optimum pH is 7.5-8.0 at 20 degrees Celsius, and 8.0-8.5 at 25 degrees Celsius in the presence of NAD+.1 Publication

    Pathwayi: L-ascorbate biosynthesis via GDP-alpha-D-mannose pathway

    This protein is involved in step 1 of the subpathway that synthesizes L-ascorbate from GDP-alpha-D-mannose.1 Publication
    Proteins known to be involved in the 5 steps of the subpathway in this organism are:
    1. GDP-mannose 3,5-epimerase 1 (GME-1), GDP-mannose 3,5-epimerase 2 (GME-2)
    2. no protein annotated in this organism
    3. no protein annotated in this organism
    4. no protein annotated in this organism
    5. no protein annotated in this organism
    This subpathway is part of the pathway L-ascorbate biosynthesis via GDP-alpha-D-mannose pathway, which is itself part of Cofactor biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-ascorbate from GDP-alpha-D-mannose, the pathway L-ascorbate biosynthesis via GDP-alpha-D-mannose pathway and in Cofactor biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei60NADBy similarity1
    Binding sitei80NADBy similarity1
    Binding sitei105Substrate; via carbonyl oxygenBy similarity1
    Active sitei175Proton acceptorBy similarity1
    Binding sitei175NADBy similarity1
    Binding sitei179NADBy similarity1
    Binding sitei204SubstrateBy similarity1
    Binding sitei226SubstrateBy similarity1
    Binding sitei307SubstrateBy similarity1
    Binding sitei357SubstrateBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi36 – 62NADBy similarityAdd BLAST27

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionIsomerase
    Biological processAscorbate biosynthesis
    LigandNAD

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-11941
    BRENDAi5.1.3.18 4460
    SABIO-RKiA3C4S4
    UniPathwayiUPA00990; UER00931

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    GDP-mannose 3,5-epimerase 1 (EC:5.1.3.18)
    Short name:
    GDP-Man 3,5-epimerase 1
    Alternative name(s):
    OsGME-1
    Gene namesi
    Name:GME-1
    Ordered Locus Names:Os10g0417600, LOC_Os10g28200
    ORF Names:OsJ_030296, OSJNBa0061K21.15
    OrganismiOryza sativa subsp. japonica (Rice)
    Taxonomic identifieri39947 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryzaOryza sativa
    Proteomesi
    • UP000059680 Componenti: Chromosome 10

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002336971 – 378GDP-mannose 3,5-epimerase 1Add BLAST378

    Proteomic databases

    PaxDbiA3C4S4

    PTM databases

    iPTMnetiA3C4S4

    Expressioni

    Gene expression databases

    ExpressionAtlasiA3C4S4 differential
    GenevisibleiA3C4S4 OS

    Interactioni

    Subunit structurei

    Homodimer.By similarity

    Protein-protein interaction databases

    STRINGi39947.LOC_Os10g28200.1

    Structurei

    3D structure databases

    ProteinModelPortaliA3C4S4
    SMRiA3C4S4
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni145 – 147Substrate bindingBy similarity3
    Regioni217 – 219Substrate bindingBy similarity3
    Regioni242 – 244Substrate bindingBy similarity3

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiKOG1429 Eukaryota
    COG0451 LUCA
    InParanoidiA3C4S4
    KOiK10046
    OMAiREAYWPA
    OrthoDBiEOG09360B69

    Family and domain databases

    CDDicd05273 GME-like_SDR_e, 1 hit
    InterProiView protein in InterPro
    IPR001509 Epimerase_deHydtase
    IPR033890 GDP-Man_epi
    IPR036291 NAD(P)-bd_dom_sf
    PfamiView protein in Pfam
    PF01370 Epimerase, 1 hit
    SUPFAMiSSF51735 SSF51735, 1 hit

    Sequencei

    Sequence statusi: Complete.

    A3C4S4-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MGSSEKNGTA YGEYTYAELE REQYWPSEKL RISITGAGGF IGSHIARRLK
    60 70 80 90 100
    SEGHYIIASD WKKNEHMTED MFCHEFHLVD LRVMDNCLKV TNGVDHVFNL
    110 120 130 140 150
    AADMGGMGFI QSNHSVIMYN NTMISFNMLE AARINGVKRF FYASSACIYP
    160 170 180 190 200
    EFKQLETNVS LKESDAWPAE PQDAYGLEKL ATEELCKHYT KDFGIECRVG
    210 220 230 240 250
    RFHNIYGPFG TWKGGREKAP AAFCRKAQTS TDRFEMWGDG LQTRSFTFID
    260 270 280 290 300
    ECVEGVLRLT KSDFREPVNI GSDEMVSMNE MAEIILSFED RELPIHHIPG
    310 320 330 340 350
    PEGVRGRNSD NTLIKEKLGW APTMKLKDGL RFTYFWIKEQ IEKEKTQGVD
    360 370
    IAGYGSSKVV STQAPVQLGS LRAADGKE
    Length:378
    Mass (Da):42,778
    Last modified:March 20, 2007 - v1
    Checksum:i4BAE83BB932C321A
    GO

    Sequence cautioni

    The sequence ABG66078 differs from that shown. Reason: Erroneous gene model prediction.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB193582 mRNA Translation: BAD66930.1
    AC016780 Genomic DNA Translation: AAM08784.1
    DP000086 Genomic DNA Translation: ABB47619.2
    DP000086 Genomic DNA Translation: ABG66078.1 Sequence problems.
    AP008216 Genomic DNA Translation: BAF26523.1
    AP014966 Genomic DNA Translation: BAT10866.1
    CM000147 Genomic DNA Translation: EAZ16087.1
    AK104822 mRNA Translation: BAG96977.1
    RefSeqiXP_015614669.1, XM_015759183.1
    UniGeneiOs.8361

    Genome annotation databases

    EnsemblPlantsiOs10t0417600-01; Os10t0417600-01; Os10g0417600
    GeneIDi4348636
    GrameneiOs10t0417600-01; Os10t0417600-01; Os10g0417600
    KEGGiosa:4348636

    Similar proteinsi

    Entry informationi

    Entry nameiGME1_ORYSJ
    AccessioniPrimary (citable) accession number: A3C4S4
    Secondary accession number(s): B7EX80
    , Q0IXP2, Q0R4F5, Q109P5, Q338B5, Q5W7P1, Q8S862
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 10, 2007
    Last sequence update: March 20, 2007
    Last modified: May 23, 2018
    This is version 80 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. Oryza sativa (rice)
      Index of Oryza sativa entries and their corresponding gene designations
    3. SIMILARITY comments
      Index of protein domains and families

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