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P25856 (G3PA1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 146. 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·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic

EC=1.2.1.13
Alternative name(s):
NADP-dependent glyceraldehydephosphate dehydrogenase A subunit 1
Gene names
Name:GAPA1
Synonyms:GAPA
Ordered Locus Names:At3g26650
ORF Names:MLJ15.4, MLJ15_5
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length396 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Involved in the photosynthetic reductive pentose phosphate pathway (Calvin-Benson cycle). Catalyzes the reduction of 1,3-diphosphoglycerate by NADPH By similarity.

Catalytic activity

D-glyceraldehyde 3-phosphate + phosphate + NADP+ = 3-phospho-D-glyceroyl phosphate + NADPH.

Pathway

Carbohydrate biosynthesis; Calvin cycle.

Subunit structure

Tetramer of either four A chains (GAPDH 2) or two A and two B chains (GAPDH 1). Ref.10 Ref.11

Subcellular location

Plastidchloroplast membrane; Peripheral membrane protein. Plastidchloroplast stroma Ref.7 Ref.9.

Tissue specificity

Expressed in leaves and stems. Ref.8

Induction

Repressed by darkness and sucrose. Ref.8

Miscellaneous

Plants contain three types of GAPDH: NAD-dependent cytosolic forms which participate in glycolysis, NAD-dependent chloroplastic forms which participate in plastidic glycolysis and NADP-depedent chloroplastic forms which participate in the photosynthetic reductive pentose phosphate pathway (Calvin-Benson cycle). All the forms are encoded by distinct genes.

Sequence similarities

Belongs to the glyceraldehyde-3-phosphate dehydrogenase family.

Sequence caution

The sequence AAD10209.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
   Biological processCalvin cycle
   Cellular componentChloroplast
Membrane
Plastid
   DomainTransit peptide
   LigandNADP
   Molecular functionOxidoreductase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processglucose metabolic process

Inferred from electronic annotation. Source: InterPro

reductive pentose-phosphate cycle

Non-traceable author statement Ref.8. Source: TAIR

response to cold

Inferred from expression pattern PubMed 16923014. Source: TAIR

response to light stimulus

Inferred from expression pattern Ref.8. Source: TAIR

response to sucrose

Inferred from expression pattern Ref.8. Source: TAIR

   Cellular_componentapoplast

Inferred from direct assay PubMed 18538804. Source: TAIR

chloroplast

Inferred from direct assay PubMed 18431481. Source: TAIR

chloroplast envelope

Inferred from direct assay PubMed 20061580. Source: TAIR

chloroplast membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

chloroplast stroma

Inferred from direct assay PubMed 16207701PubMed 18633119PubMed 20061580. Source: TAIR

chloroplast thylakoid membrane

Inferred from direct assay PubMed 15322131. Source: TAIR

membrane

Inferred from direct assay PubMed 17432890. Source: TAIR

stromule

Inferred from direct assay PubMed 16923014. Source: TAIR

   Molecular_functionNAD binding

Inferred from electronic annotation. Source: InterPro

NADP binding

Inferred from electronic annotation. Source: InterPro

glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity

Inferred from electronic annotation. Source: UniProtKB-EC

protein binding

Inferred from physical interaction PubMed 17947231. Source: IntAct

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

CP12-2Q9LZP94EBI-1554434,EBI-449218

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 6060Chloroplast By similarity
Chain61 – 396336Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic
PRO_0000010416

Regions

Nucleotide binding71 – 722NADP
Region212 – 2143Glyceraldehyde 3-phosphate binding By similarity
Region271 – 2722Glyceraldehyde 3-phosphate binding By similarity

Sites

Active site2131Nucleophile By similarity
Binding site951NADP
Binding site1401NADP; via carbonyl oxygen
Binding site2431Glyceraldehyde 3-phosphate By similarity
Binding site2581Glyceraldehyde 3-phosphate By similarity
Binding site2941Glyceraldehyde 3-phosphate By similarity
Binding site3761NADP
Site2401Activates thiol group during catalysis By similarity

Experimental info

Sequence conflict1721I → M in AAA32793. Ref.1
Sequence conflict1721I → M in AAD10209. Ref.1
Sequence conflict1721I → M in CAA66816. Ref.3

Secondary structure

...................................................................... 396
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P25856 [UniParc].

Last modified May 2, 2002. Version 3.
Checksum: FFD7FD662FB222FC

FASTA39642,490
        10         20         30         40         50         60 
MASVTFSVPK GFTEFSGLRS SSASLPFGKK LSSDEFVSIV SFQTSAMGSS GGYRKGVTEA 

        70         80         90        100        110        120 
KLKVAINGFG RIGRNFLRCW HGRKDSPLDI IAINDTGGVK QASHLLKYDS TLGIFDADVK 

       130        140        150        160        170        180 
PSGETAISVD GKIIQVVSNR NPSLLPWKEL GIDIVIEGTG VFVDREGAGK HIEAGAKKVI 

       190        200        210        220        230        240 
ITAPGKGDIP TYVVGVNADA YSHDEPIISN ASCTTNCLAP FVKVLDQKFG IIKGTMTTTH 

       250        260        270        280        290        300 
SYTGDQRLLD ASHRDLRRAR AAALNIVPTS TGAAKAVALV LPNLKGKLNG IALRVPTPNV 

       310        320        330        340        350        360 
SVVDLVVQVS KKTFAEEVNA AFRDSAEKEL KGILDVCDEP LVSVDFRCSD FSTTIDSSLT 

       370        380        390 
MVMGDDMVKV IAWYDNEWGY SQRVVDLADI VANNWK 

« Hide

References

« Hide 'large scale' references
[1]"Cloning and chromosomal mapping of nuclear genes encoding chloroplast and cytosolic glyceraldehyde-3-phosphate-dehydrogenase from Arabidopsis thaliana."
Shih M.-C., Heinrich P., Goodman H.M.
Gene 104:133-138(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
[2]Erratum
Shih M.-C., Heinrich P., Goodman H.M.
Gene 119:317-319(1992) [PubMed] [Europe PMC] [Abstract]
[3]"Sequence analysis of an 81 kb contig from Arabidopsis thaliana chromosome III."
Quigley F., Dao P., Cottet A., Mache R.
Nucleic Acids Res. 24:4313-4318(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
Strain: cv. Columbia.
Tissue: Shoot.
[4]"Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence features of the regions of 4,504,864 bp covered by sixty P1 and TAC clones."
Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.
DNA Res. 7:131-135(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Columbia.
[5]The Arabidopsis Information Resource (TAIR)
Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: cv. Columbia.
[6]"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.
[7]"Proteomics of the chloroplast envelope membranes from Arabidopsis thaliana."
Ferro M., Salvi D., Brugiere S., Miras S., Kowalski S., Louwagie M., Garin J., Joyard J., Rolland N.
Mol. Cell. Proteomics 2:325-345(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
Strain: cv. Wassilewskija.
[8]"Co-ordinated gene expression of photosynthetic glyceraldehyde-3-phosphate dehydrogenase, phosphoribulokinase, and CP12 in Arabidopsis thaliana."
Marri L., Sparla F., Pupillo P., Trost P.
J. Exp. Bot. 56:73-80(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: TISSUE SPECIFICITY, INDUCTION.
[9]"Plastidial glyceraldehyde-3-phosphate dehydrogenase deficiency leads to altered root development and affects the sugar and amino acid balance in Arabidopsis."
Munoz-Bertomeu J., Cascales-Minana B., Mulet J.M., Baroja-Fernandez E., Pozueta-Romero J., Kuhn J.M., Segura J., Ros R.
Plant Physiol. 151:541-558(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[10]"Structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase (isoform A4) from Arabidopsis thaliana in complex with NAD."
Fermani S., Sparla F., Marri L., Thumiger A., Pupillo P., Falini G., Trost P.
Acta Crystallogr. F 66:621-626(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 60-396 IN COMPLEX WITH NAD, SUBUNIT.
[11]"Conformational selection and folding-upon-binding of intrinsically disordered protein CP12 regulate photosynthetic enzymes assembly."
Fermani S., Trivelli X., Sparla F., Thumiger A., Calvaresi M., Marri L., Falini G., Zerbetto F., Trost P.
J. Biol. Chem. 287:21372-21383(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 60-396 IN COMPLEX WITH NAD, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M64114 mRNA. Translation: AAD10209.1. Different initiation.
M64117 Genomic DNA. Translation: AAA32793.1.
S45910 Genomic DNA. Translation: AAB23532.1.
X98130 Genomic DNA. Translation: CAA66816.1.
AB026648 Genomic DNA. Translation: BAB01730.1.
CP002686 Genomic DNA. Translation: AEE77191.1.
AY058140 mRNA. Translation: AAL25556.1.
AY058107 mRNA. Translation: AAL24215.1.
AF428431 mRNA. Translation: AAL16200.1.
AY075637 mRNA. Translation: AAL91645.1.
AY142053 mRNA. Translation: AAM98317.1.
PIRJQ1285.
RefSeqNP_566796.2. NM_113576.3.
UniGeneAt.20459.
At.23357.
At.3405.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3K2BX-ray2.60A/B/C/D/E/F/G/H/O/Q60-396[»]
3QV1X-ray2.00A/B/C/D/E/F60-396[»]
3RVDX-ray2.70A/B/C/D/E/F/G/H/O/Q61-396[»]
ProteinModelPortalP25856.
SMRP25856. Positions 60-396.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid7607. 6 interactions.
IntActP25856. 2 interactions.

2D gel databases

SWISS-2DPAGEP25856.
World-2DPAGE0003:P25856.

Proteomic databases

PaxDbP25856.
PRIDEP25856.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT3G26650.1; AT3G26650.1; AT3G26650.
GeneID822277.
KEGGath:AT3G26650.

Organism-specific databases

TAIRAT3G26650.

Phylogenomic databases

eggNOGCOG0057.
HOGENOMHOG000071679.
InParanoidP25856.
KOK05298.
OMAKYDSLHG.
PhylomeDBP25856.

Enzyme and pathway databases

BioCycARA:AT3G26650-MONOMER.
MetaCyc:AT3G26650-MONOMER.
BRENDA1.2.1.13. 399.
UniPathwayUPA00116.

Gene expression databases

ArrayExpressP25856.
GenevestigatorP25856.

Family and domain databases

Gene3D3.40.50.720. 1 hit.
InterProIPR020831. GlycerAld/Erythrose_P_DH.
IPR020830. GlycerAld_3-P_DH_AS.
IPR020829. GlycerAld_3-P_DH_cat.
IPR020828. GlycerAld_3-P_DH_NAD(P)-bd.
IPR006424. Glyceraldehyde-3-P_DH_1.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERPTHR10836. PTHR10836. 1 hit.
PfamPF02800. Gp_dh_C. 1 hit.
PF00044. Gp_dh_N. 1 hit.
[Graphical view]
PIRSFPIRSF000149. GAP_DH. 1 hit.
PRINTSPR00078. G3PDHDRGNASE.
SMARTSM00846. Gp_dh_N. 1 hit.
[Graphical view]
TIGRFAMsTIGR01534. GAPDH-I. 1 hit.
PROSITEPS00071. GAPDH. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP25856.

Entry information

Entry nameG3PA1_ARATH
AccessionPrimary (citable) accession number: P25856
Secondary accession number(s): Q41184, Q9LSE6
Entry history
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: May 2, 2002
Last modified: July 9, 2014
This is version 146 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names