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Q93VR3

- GME_ARATH

UniProt

Q93VR3 - GME_ARATH

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Protein
GDP-mannose 3,5-epimerase
Gene
At5g28840, F7P1.20
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - 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.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 substrate

Pathwayi

Sites

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

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi34 – 6027NAD
Add
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
Complete GO annotation...

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
Complete GO annotation...

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-epimerase
PRO_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

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.

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

« Hide 'large scale' publications
  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: May 14, 2014
This is version 87 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

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