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P25856

- G3PA1_ARATH

UniProt

P25856 - G3PA1_ARATH

Protein

Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic

Gene

GAPA1

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 147 (01 Oct 2014)
      Sequence version 3 (02 May 2002)
      Previous versions | rss
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    Functioni

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

    Catalytic activityi

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

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei95 – 951NADP2 Publications
    Binding sitei140 – 1401NADP; via carbonyl oxygen2 Publications
    Active sitei213 – 2131NucleophilePROSITE-ProRule annotation
    Sitei240 – 2401Activates thiol group during catalysisBy similarity
    Binding sitei243 – 2431Glyceraldehyde 3-phosphateBy similarity
    Binding sitei258 – 2581Glyceraldehyde 3-phosphateBy similarity
    Binding sitei294 – 2941Glyceraldehyde 3-phosphateBy similarity
    Binding sitei376 – 3761NADP2 Publications

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi71 – 722NADP2 Publications

    GO - Molecular functioni

    1. glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity Source: UniProtKB-EC
    2. NAD binding Source: InterPro
    3. NADP binding Source: InterPro
    4. protein binding Source: IntAct

    GO - Biological processi

    1. glucose metabolic process Source: InterPro
    2. reductive pentose-phosphate cycle Source: TAIR
    3. response to cold Source: TAIR
    4. response to light stimulus Source: TAIR
    5. response to sucrose Source: TAIR

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Calvin cycle

    Keywords - Ligandi

    NADP

    Enzyme and pathway databases

    BioCyciARA:AT3G26650-MONOMER.
    MetaCyc:AT3G26650-MONOMER.
    BRENDAi1.2.1.13. 399.
    UniPathwayiUPA00116.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic (EC:1.2.1.13)
    Alternative name(s):
    NADP-dependent glyceraldehydephosphate dehydrogenase A subunit 1
    Gene namesi
    Name:GAPA1
    Synonyms:GAPA
    Ordered Locus Names:At3g26650
    ORF Names:MLJ15.4, MLJ15_5
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 3

    Organism-specific databases

    TAIRiAT3G26650.

    Subcellular locationi

    GO - Cellular componenti

    1. apoplast Source: TAIR
    2. chloroplast Source: TAIR
    3. chloroplast envelope Source: TAIR
    4. chloroplast membrane Source: UniProtKB-SubCell
    5. chloroplast stroma Source: TAIR
    6. chloroplast thylakoid membrane Source: TAIR
    7. membrane Source: TAIR
    8. stromule Source: TAIR

    Keywords - Cellular componenti

    Chloroplast, Membrane, Plastid

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 6060ChloroplastBy similarityAdd
    BLAST
    Chaini61 – 396336Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplasticPRO_0000010416Add
    BLAST

    Proteomic databases

    PaxDbiP25856.
    PRIDEiP25856.

    2D gel databases

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

    Expressioni

    Tissue specificityi

    Expressed in leaves and stems.1 Publication

    Inductioni

    Repressed by darkness and sucrose.1 Publication

    Gene expression databases

    ArrayExpressiP25856.
    GenevestigatoriP25856.

    Interactioni

    Subunit structurei

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

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CP12-2Q9LZP94EBI-1554434,EBI-449218

    Protein-protein interaction databases

    BioGridi7607. 6 interactions.
    IntActiP25856. 2 interactions.

    Structurei

    Secondary structure

    1
    396
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi62 – 687
    Helixi71 – 8111
    Beta strandi87 – 948
    Helixi99 – 1079
    Turni110 – 1123
    Beta strandi119 – 12911
    Beta strandi132 – 1376
    Helixi142 – 1443
    Helixi147 – 1504
    Beta strandi154 – 1574
    Beta strandi159 – 1613
    Helixi165 – 1739
    Beta strandi177 – 1837
    Beta strandi186 – 1883
    Turni194 – 1963
    Helixi198 – 2003
    Beta strandi206 – 2094
    Helixi213 – 22917
    Beta strandi231 – 24111
    Beta strandi248 – 2503
    Turni256 – 2594
    Helixi262 – 2643
    Beta strandi267 – 2693
    Helixi273 – 2808
    Helixi282 – 2843
    Turni285 – 2873
    Beta strandi288 – 2969
    Beta strandi301 – 31111
    Helixi315 – 32713
    Turni328 – 3336
    Beta strandi334 – 3374
    Helixi343 – 3464
    Beta strandi352 – 3565
    Helixi357 – 3593
    Beta strandi361 – 3633
    Turni364 – 3663
    Beta strandi367 – 3748
    Helixi378 – 39316

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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[»]
    ProteinModelPortaliP25856.
    SMRiP25856. Positions 60-396.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP25856.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni212 – 2143Glyceraldehyde 3-phosphate bindingBy similarity
    Regioni271 – 2722Glyceraldehyde 3-phosphate bindingBy similarity

    Sequence similaritiesi

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG0057.
    HOGENOMiHOG000071679.
    InParanoidiP25856.
    KOiK05298.
    OMAiKYDSLHG.
    PhylomeDBiP25856.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR020831. 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]
    PANTHERiPTHR10836. PTHR10836. 1 hit.
    PfamiPF02800. Gp_dh_C. 1 hit.
    PF00044. Gp_dh_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000149. GAP_DH. 1 hit.
    PRINTSiPR00078. G3PDHDRGNASE.
    SMARTiSM00846. Gp_dh_N. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR01534. GAPDH-I. 1 hit.
    PROSITEiPS00071. GAPDH. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P25856-1 [UniParc]FASTAAdd to Basket

    « Hide

    MASVTFSVPK GFTEFSGLRS SSASLPFGKK LSSDEFVSIV SFQTSAMGSS    50
    GGYRKGVTEA KLKVAINGFG RIGRNFLRCW HGRKDSPLDI IAINDTGGVK 100
    QASHLLKYDS TLGIFDADVK PSGETAISVD GKIIQVVSNR NPSLLPWKEL 150
    GIDIVIEGTG VFVDREGAGK HIEAGAKKVI ITAPGKGDIP TYVVGVNADA 200
    YSHDEPIISN ASCTTNCLAP FVKVLDQKFG IIKGTMTTTH SYTGDQRLLD 250
    ASHRDLRRAR AAALNIVPTS TGAAKAVALV LPNLKGKLNG IALRVPTPNV 300
    SVVDLVVQVS KKTFAEEVNA AFRDSAEKEL KGILDVCDEP LVSVDFRCSD 350
    FSTTIDSSLT MVMGDDMVKV IAWYDNEWGY SQRVVDLADI VANNWK 396
    Length:396
    Mass (Da):42,490
    Last modified:May 2, 2002 - v3
    Checksum:iFFD7FD662FB222FC
    GO

    Sequence cautioni

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

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti172 – 1721I → M in AAA32793. (PubMed:1916285)Curated
    Sequence conflicti172 – 1721I → M in AAD10209. (PubMed:1916285)Curated
    Sequence conflicti172 – 1721I → M in CAA66816. (PubMed:8932388)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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.
    PIRiJQ1285.
    RefSeqiNP_566796.2. NM_113576.3.
    UniGeneiAt.20459.
    At.23357.
    At.3405.

    Genome annotation databases

    EnsemblPlantsiAT3G26650.1; AT3G26650.1; AT3G26650.
    GeneIDi822277.
    KEGGiath:AT3G26650.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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 .
    PIRi JQ1285.
    RefSeqi NP_566796.2. NM_113576.3.
    UniGenei At.20459.
    At.23357.
    At.3405.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3K2B X-ray 2.60 A/B/C/D/E/F/G/H/O/Q 60-396 [» ]
    3QV1 X-ray 2.00 A/B/C/D/E/F 60-396 [» ]
    3RVD X-ray 2.70 A/B/C/D/E/F/G/H/O/Q 61-396 [» ]
    ProteinModelPortali P25856.
    SMRi P25856. Positions 60-396.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 7607. 6 interactions.
    IntActi P25856. 2 interactions.

    2D gel databases

    SWISS-2DPAGE P25856.
    World-2DPAGE 0003:P25856.

    Proteomic databases

    PaxDbi P25856.
    PRIDEi P25856.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT3G26650.1 ; AT3G26650.1 ; AT3G26650 .
    GeneIDi 822277.
    KEGGi ath:AT3G26650.

    Organism-specific databases

    TAIRi AT3G26650.

    Phylogenomic databases

    eggNOGi COG0057.
    HOGENOMi HOG000071679.
    InParanoidi P25856.
    KOi K05298.
    OMAi KYDSLHG.
    PhylomeDBi P25856.

    Enzyme and pathway databases

    UniPathwayi UPA00116 .
    BioCyci ARA:AT3G26650-MONOMER.
    MetaCyc:AT3G26650-MONOMER.
    BRENDAi 1.2.1.13. 399.

    Miscellaneous databases

    EvolutionaryTracei P25856.

    Gene expression databases

    ArrayExpressi P25856.
    Genevestigatori P25856.

    Family and domain databases

    Gene3Di 3.40.50.720. 1 hit.
    InterProi IPR020831. 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 ]
    PANTHERi PTHR10836. PTHR10836. 1 hit.
    Pfami PF02800. Gp_dh_C. 1 hit.
    PF00044. Gp_dh_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000149. GAP_DH. 1 hit.
    PRINTSi PR00078. G3PDHDRGNASE.
    SMARTi SM00846. Gp_dh_N. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR01534. GAPDH-I. 1 hit.
    PROSITEi PS00071. GAPDH. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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. "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.
    3. "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.
    4. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    5. "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.
    6. "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.
    7. "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.
    8. "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.
    9. "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.
    10. "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.

    Entry informationi

    Entry nameiG3PA1_ARATH
    AccessioniPrimary (citable) accession number: P25856
    Secondary accession number(s): Q41184, Q9LSE6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1992
    Last sequence update: May 2, 2002
    Last modified: October 1, 2014
    This is version 147 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    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.

    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