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Q93VR3 (GME_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 79. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
GDP-mannose 3,5-epimerase
Short name=GDP-Man 3,5-epimerase
EC=5.1.3.18
Gene names
Ordered Locus Names:At5g28840
ORF Names:F7P1.20
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length377 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.6

Catalytic activity

GDP-mannose = GDP-L-galactose. Ref.5 Ref.6

Cofactor

NAD. Ref.5

Enzyme regulation

Inhibited by GDP and GDP-D-glucose. Ref.6

Pathway

Cofactor biosynthesis; L-ascorbate biosynthesis via GDP-alpha-D-mannose pathway; L-ascorbate from GDP-alpha-D-mannose: step 1/5. Ref.4

Subunit structure

Homodimer. Interacts with chaperone Hsc70-3 protein, which may regulate epimerase activity. Ref.5 Ref.8

Sequence similarities

Belongs to the sugar epimerase family.

Biophysicochemical properties

Kinetic parameters:

KM=4.5 µM for GDP-mannose Ref.6

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

Ontologies

Keywords
   Biological processAscorbate biosynthesis
   LigandNAD
Nucleotide-binding
   Molecular functionIsomerase
   PTMPhosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processL-ascorbic acid biosynthetic process

Traceable author statement Ref.6. Source: TAIR

   Cellular_componentcytosol

Inferred from direct assay PubMed 21166475. Source: TAIR

   Molecular_functionGDP-mannose 3,5-epimerase activity

Inferred from direct assay Ref.5. Source: TAIR

NAD binding

Traceable author statement Ref.6. Source: TAIR

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 377377GDP-mannose 3,5-epimerase
PRO_0000183267

Regions

Nucleotide binding34 – 6027NAD
Region143 – 1453Substrate binding
Region216 – 2183Substrate binding
Region241 – 2433Substrate binding

Sites

Active site1741Proton acceptor By similarity
Binding site581NAD
Binding site781NAD
Binding site1031Substrate; via carbonyl oxygen
Binding site1741NAD
Binding site1781NAD
Binding site2031Substrate
Binding site2251Substrate
Binding site3061Substrate
Binding site3561Substrate

Amino acid modifications

Modified residue3691Phosphoserine Ref.7

Experimental info

Mutagenesis1451C → A: Loss of activity. Ref.8
Mutagenesis1451C → S: Strong reduction of activity. Ref.8
Mutagenesis1741Y → F: Loss of activity. Ref.8
Mutagenesis1781K → R: Strong reduction of activity. Ref.8
Mutagenesis2171K → A: Loss of activity. Ref.8
Mutagenesis3061R → A: Strong reduction of activity. Ref.8

Secondary structure

1 ............................................................ 377
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q93VR3 [UniParc].

Last modified December 1, 2001. Version 1.
Checksum: 91C6C4A4C34CCE57

FASTA37742,758
        10         20         30         40         50         60 
MGTTNGTDYG AYTYKELERE QYWPSENLKI SITGAGGFIA SHIARRLKHE GHYVIASDWK 

        70         80         90        100        110        120 
KNEHMTEDMF CDEFHLVDLR VMENCLKVTE GVDHVFNLAA DMGGMGFIQS NHSVIMYNNT 

       130        140        150        160        170        180 
MISFNMIEAA RINGIKRFFY ASSACIYPEF KQLETTNVSL KESDAWPAEP QDAYGLEKLA 

       190        200        210        220        230        240 
TEELCKHYNK DFGIECRIGR FHNIYGPFGT WKGGREKAPA AFCRKAQTST DRFEMWGDGL 

       250        260        270        280        290        300 
QTRSFTFIDE CVEGVLRLTK SDFREPVNIG SDEMVSMNEM AEMVLSFEEK KLPIHHIPGP 

       310        320        330        340        350        360 
EGVRGRNSDN NLIKEKLGWA PNMRLKEGLR ITYFWIKEQI EKEKAKGSDV SLYGSSKVVG 

       370 
TQAPVQLGSL RAADGKE

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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. expand/collapse author list , 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, MASS SPECTROMETRY.
Strain: cv. Columbia.
Tissue: Seedling.
[8]"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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		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.
IPIIPI00536932.
RefSeqNP_001190417.1. NM_001203488.1.
NP_198236.1. NM_122767.3.
UniGeneAt.21733.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2C54X-ray1.50A/B1-377[»]
2C59X-ray2.00A/B1-377[»]
2C5AX-ray1.40A/B1-377[»]
2C5EX-ray1.70A/B1-377[»]
ProteinModelPortalQ93VR3.
SMRQ93VR3. Positions 13-375.
ModBaseSearch...

Proteomic databases

PaxDbQ93VR3.
PRIDEQ93VR3.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT5G28840.1; AT5G28840.1; AT5G28840.
AT5G28840.2; AT5G28840.2; AT5G28840.
GeneID833002.
KEGGath:AT5G28840.

Organism-specific databases

TAIRAt5g28840.

Phylogenomic databases

eggNOGCOG0451.
HOGENOMHOG000168017.
InParanoidQ93VR3.
KOK10046.
OMARKAQTST.
PhylomeDBQ93VR3.
ProtClustDBPLN02695.

Enzyme and pathway databases

BioCycARA:AT5G28840-MONOMER.
MetaCyc:AT5G28840-MONOMER.
UniPathwayUPA00990; UER00931.

Gene expression databases

ArrayExpressQ93VR3.
GenevestigatorQ93VR3.
GermOnlineAT5G28840. Arabidopsis thaliana.

Family and domain databases

Gene3D3.40.50.720. 1 hit.
InterProIPR001509. Epimerase_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamPF01370. Epimerase. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ93VR3.

Entry information

Entry nameGME_ARATH
AccessionPrimary (citable) accession number: Q93VR3
Entry history
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: December 1, 2001
Last modified: May 1, 2013
This is version 79 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents