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Q93VR3

- GME_ARATH

UniProt

Q93VR3 - GME_ARATH

Protein

GDP-mannose 3,5-epimerase

Gene

At5g28840

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 88 (01 Oct 2014)
      Sequence version 1 (01 Dec 2001)
      Previous versions | rss
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    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.2 Publications

    Cofactori

    NAD.1 Publication

    Enzyme regulationi

    Inhibited by GDP and GDP-D-glucose.1 Publication

    Kineticsi

    1. KM=4.5 µM for GDP-mannose1 Publication

    Vmax=1.76 µmol/h/mg enzyme with GDP-mannose as substrate1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei58 – 581NAD1 Publication
    Binding sitei78 – 781NAD1 Publication
    Binding sitei103 – 1031Substrate; via carbonyl oxygen
    Active sitei174 – 1741Proton acceptorBy similarity
    Binding sitei174 – 1741NAD1 Publication
    Binding sitei178 – 1781NAD1 Publication
    Binding sitei203 – 2031Substrate
    Binding sitei225 – 2251Substrate
    Binding sitei306 – 3061Substrate
    Binding sitei356 – 3561Substrate

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi34 – 6027NAD1 PublicationAdd
    BLAST

    GO - Molecular functioni

    1. GDP-mannose 3,5-epimerase activity Source: TAIR
    2. NAD binding Source: TAIR

    GO - Biological processi

    1. L-ascorbic acid biosynthetic process Source: TAIR

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Ascorbate biosynthesis

    Keywords - Ligandi

    NAD, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciARA:AT5G28840-MONOMER.
    ARA:GQT-2356-MONOMER.
    MetaCyc:AT5G28840-MONOMER.
    SABIO-RKQ93VR3.
    UniPathwayiUPA00990; UER00931.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    GDP-mannose 3,5-epimerase (EC:5.1.3.18)
    Short name:
    GDP-Man 3,5-epimerase
    Gene namesi
    Ordered Locus Names:At5g28840
    ORF Names:F7P1.20
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 5

    Organism-specific databases

    TAIRiAT5G28840.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: TAIR

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi145 – 1451C → A: Loss of activity. 1 Publication
    Mutagenesisi145 – 1451C → S: Strong reduction of activity. 1 Publication
    Mutagenesisi174 – 1741Y → F: Loss of activity. 1 Publication
    Mutagenesisi178 – 1781K → R: Strong reduction of activity. 1 Publication
    Mutagenesisi217 – 2171K → A: Loss of activity. 1 Publication
    Mutagenesisi306 – 3061R → A: Strong reduction of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 377376GDP-mannose 3,5-epimerasePRO_0000183267Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylglycine1 Publication
    Modified residuei369 – 3691Phosphoserine1 Publication

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    PaxDbiQ93VR3.
    PRIDEiQ93VR3.

    Expressioni

    Gene expression databases

    ArrayExpressiQ93VR3.
    GenevestigatoriQ93VR3.

    Interactioni

    Subunit structurei

    Homodimer. Interacts with chaperone Hsc70-3 protein, which may regulate epimerase activity.2 Publications

    Structurei

    Secondary structure

    1
    377
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi29 – 335
    Turni34 – 363
    Helixi38 – 4912
    Beta strandi53 – 608
    Beta strandi63 – 653
    Helixi67 – 693
    Beta strandi72 – 765
    Helixi82 – 898
    Beta strandi93 – 975
    Helixi105 – 1084
    Helixi112 – 13221
    Beta strandi136 – 1438
    Helixi144 – 1463
    Helixi149 – 1513
    Beta strandi152 – 1576
    Helixi162 – 1654
    Beta strandi166 – 1683
    Beta strandi170 – 1723
    Helixi173 – 19220
    Beta strandi195 – 2017
    Beta strandi212 – 2143
    Helixi218 – 22811
    Beta strandi233 – 2375
    Beta strandi242 – 2443
    Helixi248 – 26013
    Beta strandi267 – 2693
    Beta strandi274 – 2763
    Helixi277 – 28610
    Turni287 – 2893
    Beta strandi294 – 2974
    Helixi311 – 3177
    Helixi325 – 34622
    Helixi350 – 3545

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2C54X-ray1.50A/B1-377[»]
    2C59X-ray2.00A/B1-377[»]
    2C5AX-ray1.40A/B1-377[»]
    2C5EX-ray1.70A/B1-377[»]
    ProteinModelPortaliQ93VR3.
    SMRiQ93VR3. Positions 13-375.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ93VR3.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni143 – 1453Substrate binding
    Regioni216 – 2183Substrate binding
    Regioni241 – 2433Substrate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0451.
    HOGENOMiHOG000168017.
    InParanoidiQ93VR3.
    KOiK10046.
    OMAiGRNSDNN.
    PhylomeDBiQ93VR3.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR001509. Epimerase_deHydtase.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF01370. Epimerase. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q93VR3-1 [UniParc]FASTAAdd to Basket

    « Hide

    MGTTNGTDYG AYTYKELERE QYWPSENLKI SITGAGGFIA SHIARRLKHE    50
    GHYVIASDWK KNEHMTEDMF CDEFHLVDLR VMENCLKVTE GVDHVFNLAA 100
    DMGGMGFIQS NHSVIMYNNT MISFNMIEAA RINGIKRFFY ASSACIYPEF 150
    KQLETTNVSL KESDAWPAEP QDAYGLEKLA TEELCKHYNK DFGIECRIGR 200
    FHNIYGPFGT WKGGREKAPA AFCRKAQTST DRFEMWGDGL QTRSFTFIDE 250
    CVEGVLRLTK SDFREPVNIG SDEMVSMNEM AEMVLSFEEK KLPIHHIPGP 300
    EGVRGRNSDN NLIKEKLGWA PNMRLKEGLR ITYFWIKEQI EKEKAKGSDV 350
    SLYGSSKVVG TQAPVQLGSL RAADGKE 377
    Length:377
    Mass (Da):42,758
    Last modified:December 1, 2001 - v1
    Checksum:i91C6C4A4C34CCE57
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF272706 Genomic DNA. No translation available.
    CP002688 Genomic DNA. Translation: AED93843.1.
    CP002688 Genomic DNA. Translation: AED93844.1.
    AY057660 mRNA. Translation: AAL15291.1.
    AY057694 mRNA. Translation: AAL15324.1.
    AY116953 mRNA. Translation: AAM51587.1.
    RefSeqiNP_001190417.1. NM_001203488.1.
    NP_198236.1. NM_122767.3.
    UniGeneiAt.21733.

    Genome annotation databases

    EnsemblPlantsiAT5G28840.1; AT5G28840.1; AT5G28840.
    AT5G28840.2; AT5G28840.2; AT5G28840.
    GeneIDi833002.
    KEGGiath:AT5G28840.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF272706 Genomic DNA. No translation available.
    CP002688 Genomic DNA. Translation: AED93843.1 .
    CP002688 Genomic DNA. Translation: AED93844.1 .
    AY057660 mRNA. Translation: AAL15291.1 .
    AY057694 mRNA. Translation: AAL15324.1 .
    AY116953 mRNA. Translation: AAM51587.1 .
    RefSeqi NP_001190417.1. NM_001203488.1.
    NP_198236.1. NM_122767.3.
    UniGenei At.21733.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2C54 X-ray 1.50 A/B 1-377 [» ]
    2C59 X-ray 2.00 A/B 1-377 [» ]
    2C5A X-ray 1.40 A/B 1-377 [» ]
    2C5E X-ray 1.70 A/B 1-377 [» ]
    ProteinModelPortali Q93VR3.
    SMRi Q93VR3. Positions 13-375.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PaxDbi Q93VR3.
    PRIDEi Q93VR3.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT5G28840.1 ; AT5G28840.1 ; AT5G28840 .
    AT5G28840.2 ; AT5G28840.2 ; AT5G28840 .
    GeneIDi 833002.
    KEGGi ath:AT5G28840.

    Organism-specific databases

    TAIRi AT5G28840.

    Phylogenomic databases

    eggNOGi COG0451.
    HOGENOMi HOG000168017.
    InParanoidi Q93VR3.
    KOi K10046.
    OMAi GRNSDNN.
    PhylomeDBi Q93VR3.

    Enzyme and pathway databases

    UniPathwayi UPA00990 ; UER00931 .
    BioCyci ARA:AT5G28840-MONOMER.
    ARA:GQT-2356-MONOMER.
    MetaCyc:AT5G28840-MONOMER.
    SABIO-RK Q93VR3.

    Miscellaneous databases

    EvolutionaryTracei Q93VR3.

    Gene expression databases

    ArrayExpressi Q93VR3.
    Genevestigatori Q93VR3.

    Family and domain databases

    Gene3Di 3.40.50.720. 1 hit.
    InterProi IPR001509. Epimerase_deHydtase.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view ]
    Pfami PF01370. Epimerase. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana."
      Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.
      , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.
      Nature 408:823-826(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    2. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    3. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    4. "The biosynthetic pathway of vitamin C in higher plants."
      Wheeler G.L., Jones M.A., Smirnoff N.
      Nature 393:365-369(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: PATHWAY.
    5. "Partial purification and identification of GDP-mannose 3',5'-epimerase of Arabidopsis thaliana, a key enzyme of the plant vitamin C pathway."
      Wolucka B.A., Persiau G., Van Doorsselaere J., Davey M.W., Demol H., Vandekerckhove J., Van Montagu M., Zabeau M., Boerjan W.
      Proc. Natl. Acad. Sci. U.S.A. 98:14843-14848(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY, ENZYME ACTIVITY, COFACTOR, SUBUNIT, INTERACTION WITH HSC70-3.
    6. "GDP-mannose 3',5'-epimerase forms GDP-L-gulose, a putative intermediate for the de novo biosynthesis of vitamin C in plants."
      Wolucka B.A., Van Montagu M.
      J. Biol. Chem. 278:47483-47490(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, ENZYME ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
    7. "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks."
      Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S.
      Plant Physiol. 150:889-903(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-369, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
      Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
      Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT GLY-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
    9. "Structure and function of GDP-mannose-3',5'-epimerase: an enzyme which performs three chemical reactions at the same active site."
      Major L.L., Wolucka B.A., Naismith J.H.
      J. Am. Chem. Soc. 127:18309-18320(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) OF 1-377 IN COMPLEX WITH NAD AND SUBSTRATES, SUBUNIT, MUTAGENESIS OF CYS-145; TYR-174; LYS-178; LYS-217 AND ARG-306.

    Entry informationi

    Entry nameiGME_ARATH
    AccessioniPrimary (citable) accession number: Q93VR3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 30, 2005
    Last sequence update: December 1, 2001
    Last modified: October 1, 2014
    This is version 88 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    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