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Protein

GDP-mannose 3,5-epimerase

Gene

At5g28840

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: 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
  1. Vmax=1.76 µmol/h/mg enzyme with GDP-mannose as substrate1 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 (At5g28840)
  2. GDP-L-galactose phosphorylase 1 (VTC2), GDP-L-galactose phosphorylase 2 (VTC5)
  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 sitei58NAD1 Publication1
Binding sitei78NAD1 Publication1
Binding sitei103Substrate; via carbonyl oxygen1
Active sitei174Proton acceptorBy similarity1
Binding sitei174NAD1 Publication1
Binding sitei178NAD1 Publication1
Binding sitei203Substrate1
Binding sitei225Substrate1
Binding sitei306Substrate1
Binding sitei356Substrate1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi34 – 60NAD1 PublicationAdd BLAST27

GO - Molecular functioni

  • GDP-mannose 3,5-epimerase activity Source: TAIR
  • NAD binding Source: TAIR

GO - Biological processi

  • 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.
MetaCyc:AT5G28840-MONOMER.
BRENDAi5.1.3.18. 399.
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
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G28840.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: TAIR
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi145C → A: Loss of activity. 1 Publication1
Mutagenesisi145C → S: Strong reduction of activity. 1 Publication1
Mutagenesisi174Y → F: Loss of activity. 1 Publication1
Mutagenesisi178K → R: Strong reduction of activity. 1 Publication1
Mutagenesisi217K → A: Loss of activity. 1 Publication1
Mutagenesisi306R → A: Strong reduction of activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00001832672 – 377GDP-mannose 3,5-epimeraseAdd BLAST376

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylglycineCombined sources1
Modified residuei369PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiQ93VR3.
PRIDEiQ93VR3.

PTM databases

iPTMnetiQ93VR3.

Expressioni

Gene expression databases

ExpressionAtlasiQ93VR3. baseline and differential.
GenevisibleiQ93VR3. AT.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi3702.AT5G28840.1.

Structurei

Secondary structure

1377
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi29 – 33Combined sources5
Turni34 – 36Combined sources3
Helixi38 – 49Combined sources12
Beta strandi53 – 60Combined sources8
Beta strandi63 – 65Combined sources3
Helixi67 – 69Combined sources3
Beta strandi72 – 76Combined sources5
Helixi82 – 89Combined sources8
Beta strandi93 – 97Combined sources5
Helixi105 – 108Combined sources4
Helixi112 – 132Combined sources21
Beta strandi136 – 143Combined sources8
Helixi144 – 146Combined sources3
Helixi149 – 151Combined sources3
Beta strandi152 – 157Combined sources6
Helixi162 – 165Combined sources4
Beta strandi166 – 168Combined sources3
Beta strandi170 – 172Combined sources3
Helixi173 – 192Combined sources20
Beta strandi195 – 201Combined sources7
Beta strandi212 – 214Combined sources3
Helixi218 – 228Combined sources11
Beta strandi233 – 237Combined sources5
Beta strandi242 – 244Combined sources3
Helixi248 – 260Combined sources13
Beta strandi267 – 269Combined sources3
Beta strandi274 – 276Combined sources3
Helixi277 – 286Combined sources10
Turni287 – 289Combined sources3
Beta strandi294 – 297Combined sources4
Helixi311 – 317Combined sources7
Helixi325 – 346Combined sources22
Helixi350 – 354Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ93VR3.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni143 – 145Substrate binding3
Regioni216 – 218Substrate binding3
Regioni241 – 243Substrate binding3

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1429. Eukaryota.
COG0451. LUCA.
HOGENOMiHOG000168017.
InParanoidiQ93VR3.
KOiK10046.
OMAiNYGAFTY.
OrthoDBiEOG09360B69.
PhylomeDBiQ93VR3.

Family and domain databases

CDDicd05273. GME-like_SDR_e. 1 hit.
Gene3Di3.40.50.720. 1 hit.
InterProiIPR001509. Epimerase_deHydtase.
IPR033890. GDP-Man_epi.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF01370. Epimerase. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.

Sequencei

Sequence statusi: Complete.

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

Q93VR3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGTTNGTDYG AYTYKELERE QYWPSENLKI SITGAGGFIA SHIARRLKHE
60 70 80 90 100
GHYVIASDWK KNEHMTEDMF CDEFHLVDLR VMENCLKVTE GVDHVFNLAA
110 120 130 140 150
DMGGMGFIQS NHSVIMYNNT MISFNMIEAA RINGIKRFFY ASSACIYPEF
160 170 180 190 200
KQLETTNVSL KESDAWPAEP QDAYGLEKLA TEELCKHYNK DFGIECRIGR
210 220 230 240 250
FHNIYGPFGT WKGGREKAPA AFCRKAQTST DRFEMWGDGL QTRSFTFIDE
260 270 280 290 300
CVEGVLRLTK SDFREPVNIG SDEMVSMNEM AEMVLSFEEK KLPIHHIPGP
310 320 330 340 350
EGVRGRNSDN NLIKEKLGWA PNMRLKEGLR ITYFWIKEQI EKEKAKGSDV
360 370
SLYGSSKVVG TQAPVQLGSL RAADGKE
Length:377
Mass (Da):42,758
Last modified:December 1, 2001 - v1
Checksum:i91C6C4A4C34CCE57
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_122767.4.
UniGeneiAt.21733.

Genome annotation databases

EnsemblPlantsiAT5G28840.1; AT5G28840.1; AT5G28840.
AT5G28840.2; AT5G28840.2; AT5G28840.
GeneIDi833002.
GrameneiAT5G28840.1; AT5G28840.1; AT5G28840.
AT5G28840.2; AT5G28840.2; AT5G28840.
KEGGiath:AT5G28840.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_122767.4.
UniGeneiAt.21733.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT5G28840.1.

PTM databases

iPTMnetiQ93VR3.

Proteomic databases

PaxDbiQ93VR3.
PRIDEiQ93VR3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G28840.1; AT5G28840.1; AT5G28840.
AT5G28840.2; AT5G28840.2; AT5G28840.
GeneIDi833002.
GrameneiAT5G28840.1; AT5G28840.1; AT5G28840.
AT5G28840.2; AT5G28840.2; AT5G28840.
KEGGiath:AT5G28840.

Organism-specific databases

TAIRiAT5G28840.

Phylogenomic databases

eggNOGiKOG1429. Eukaryota.
COG0451. LUCA.
HOGENOMiHOG000168017.
InParanoidiQ93VR3.
KOiK10046.
OMAiNYGAFTY.
OrthoDBiEOG09360B69.
PhylomeDBiQ93VR3.

Enzyme and pathway databases

UniPathwayiUPA00990; UER00931.
BioCyciARA:AT5G28840-MONOMER.
MetaCyc:AT5G28840-MONOMER.
BRENDAi5.1.3.18. 399.
SABIO-RKQ93VR3.

Miscellaneous databases

EvolutionaryTraceiQ93VR3.
PROiQ93VR3.

Gene expression databases

ExpressionAtlasiQ93VR3. baseline and differential.
GenevisibleiQ93VR3. AT.

Family and domain databases

CDDicd05273. GME-like_SDR_e. 1 hit.
Gene3Di3.40.50.720. 1 hit.
InterProiIPR001509. Epimerase_deHydtase.
IPR033890. GDP-Man_epi.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF01370. Epimerase. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
ProtoNetiSearch...

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: November 30, 2016
This is version 104 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.