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Protein

Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic

Gene

GAPC1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Key enzyme in glycolysis that catalyzes the first step of the pathway by converting D-glyceraldehyde 3-phosphate (G3P) into 3-phospho-D-glyceroyl phosphate. Essential for the maintenance of cellular ATP levels and carbohydrate metabolism. Required for full fertility (PubMed:18820081). Involved in response to oxidative stress by mediating plant responses to abscisic acid (ABA) and water deficits through the activation of PLDDELTA and production of phosphatidic acid (PA), a multifunctional stress signaling lipid in plants (PubMed:22589465). Associates with FBA6 to the outer mitochondrial membrane, in a redox-dependent manner, leading to binding and bundling of actin. Actin binding and bundling occurs under oxidizing conditions and is reversible under reducing conditions. May be part of a redox-dependent retrograde signal transduction network for adaptation upon oxidative stress (PubMed:23316205). Binds DNA in vitro.3 Publications

Catalytic activityi

D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH.PROSITE-ProRule annotation1 Publication

Enzyme regulationi

Inhibition by oxidized glutathione (GSSG), S-nitrosoglutathione (GSNO), hydrogen peroxide and sodium nitroprusside (SNP).4 Publications

Pathwayi: glycolysis

This protein is involved in step 1 of the subpathway that synthesizes pyruvate from D-glyceraldehyde 3-phosphate.
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. Glyceraldehyde-3-phosphate dehydrogenase GAPC2, cytosolic (GAPC2), Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic (GAPC1)
  2. Phosphoglycerate kinase 3, cytosolic (PGK3)
  3. Probable 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 2 (At3g08590), 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 1 (PGM1)
  4. Enolase 1, chloroplastic (ENO1), Cytosolic enolase 3 (ENO3), Bifunctional enolase 2/transcriptional activator (ENO2)
  5. Pyruvate kinase (AXX17_At5g51800), Pyruvate kinase (AXX17_At3g24740), Pyruvate kinase (AXX17_At3g50280), Pyruvate kinase (AXX17_ATUG04870), Pyruvate kinase (At5g08570), Pyruvate kinase (At5g56350), Pyruvate kinase (At3g25960), Pyruvate kinase (At5g63680), Pyruvate kinase (F1I16_60), Pyruvate kinase (AXX17_At3g50440), Plastidial pyruvate kinase 3, chloroplastic (PKP3), Pyruvate kinase (At3g52990), Pyruvate kinase (AXX17_At3g28070), Pyruvate kinase (At2g36580), Pyruvate kinase (AXX17_At3g47400), Pyruvate kinase, Probable pyruvate kinase, cytosolic isozyme (At4g26390), Pyruvate kinase (F8J2_160), Pyruvate kinase (At3g52990), Pyruvate kinase (AXX17_At3g03460), Plastidial pyruvate kinase 2 (PKP2), Pyruvate kinase (T11I18.16), Pyruvate kinase (AXX17_At4g30430), Pyruvate kinase (F1I16_220), Plastidial pyruvate kinase 1, chloroplastic (PKP1), Pyruvate kinase (AXX17_At1g33230), Pyruvate kinase (At5g63680), Pyruvate kinase, Plastidial pyruvate kinase 4, chloroplastic (PKP4)
This subpathway is part of the pathway glycolysis, which is itself part of Carbohydrate degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyruvate from D-glyceraldehyde 3-phosphate, the pathway glycolysis and in Carbohydrate degradation.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei37NADBy similarity1
Binding sitei84NAD; via carbonyl oxygenBy similarity1
Active sitei156Nucleophile1 Publication1
Sitei183Activates thiol group during catalysisBy similarity1
Binding sitei186Glyceraldehyde 3-phosphateBy similarity1
Binding sitei238Glyceraldehyde 3-phosphateBy similarity1
Binding sitei320NADBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi15 – 16NADBy similarity2

GO - Molecular functioni

  • copper ion binding Source: TAIR
  • DNA binding Source: UniProtKB-KW
  • glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity Source: TAIR
  • glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity Source: TAIR
  • NAD binding Source: InterPro
  • NADP binding Source: InterPro

GO - Biological processi

  • fruit development Source: TAIR
  • gluconeogenesis Source: TAIR
  • glycolytic process Source: TAIR
  • response to cadmium ion Source: TAIR
  • response to heat Source: TAIR
  • response to hydrogen peroxide Source: TAIR
  • response to oxidative stress Source: TAIR
  • response to redox state Source: TAIR
  • response to salt stress Source: TAIR
  • response to sucrose Source: TAIR
  • seed development Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Glycolysis, Stress response

Keywords - Ligandi

DNA-binding, NAD

Enzyme and pathway databases

BRENDAi1.2.1.12. 399.
ReactomeiR-ATH-70171. Glycolysis.
R-ATH-70263. Gluconeogenesis.
UniPathwayiUPA00109; UER00184.

Names & Taxonomyi

Protein namesi
Recommended name:
Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic (EC:1.2.1.12)
Alternative name(s):
NAD-dependent glyceraldehydephosphate dehydrogenase C subunit 1
Gene namesi
Name:GAPC1
Synonyms:GAPC, GAPDH
Ordered Locus Names:At3g04120
ORF Names:T6K12.26
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G04120.

Subcellular locationi

GO - Cellular componenti

  • apoplast Source: TAIR
  • chloroplast Source: TAIR
  • cytosol Source: TAIR
  • membrane Source: TAIR
  • mitochondrial envelope Source: TAIR
  • mitochondrion Source: TAIR
  • nucleus Source: TAIR
  • plasma membrane Source: TAIR
  • vacuolar membrane Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

Delayed growth, small siliques with defects in fertility, and alterations of seed and fruit development. Reduced respiratory rates, pyruvate levels and Krebs cycle intermediates. Increased reactive oxygen species levels.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi156C → S: Loss of activity. Loss of glutathionylation. 1 Publication1
Mutagenesisi160C → S: No effect on the activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001455941 – 338Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolicAdd BLAST338

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei156S-glutathionyl cysteine; transient; alternate1 Publication1
Modified residuei156S-nitrosocysteine; transient; alternateBy similarity1
Modified residuei160S-nitrosocysteine; transientBy similarity1

Post-translational modificationi

S-glutathionylation at Cys-156 in the presence of oxidized glutathione (GSSG). S-nitrosylation in the presence of S-nitrosoglutathione (GSNO) or sodium nitroprusside (SNP). These reactions may be both a protective mechanism against irreversible oxidation and a mean to store inhibited enzyme in a recoverable form. Glutathionylation is reversed by both glutaredoxins and thioredoxins in vitro.1 Publication

Keywords - PTMi

Glutathionylation, S-nitrosylation

Proteomic databases

PaxDbiP25858.
PRIDEiP25858.

PTM databases

iPTMnetiP25858.

Expressioni

Tissue specificityi

Expressed in leaves, stems and siliques and at lower levels in roots and flowers.1 Publication

Inductioni

Not repressed by darkness or sucrose.1 Publication

Gene expression databases

GenevisibleiP25858. AT.

Interactioni

Subunit structurei

Homotetramer (By similarity). Interacts with PLDDELTA (PubMed:22589465). Interacts with FBA6 and VDAC3 (PubMed:23316205).By similarity2 Publications

Protein-protein interaction databases

BioGridi4902. 10 interactors.
IntActiP25858. 2 interactors.
MINTiMINT-8060263.
STRINGi3702.AT3G04120.1.

Structurei

Secondary structure

1338
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi7 – 12Combined sources6
Helixi15 – 26Combined sources12
Beta strandi31 – 36Combined sources6
Helixi42 – 50Combined sources9
Turni53 – 55Combined sources3
Beta strandi63 – 66Combined sources4
Turni67 – 69Combined sources3
Beta strandi70 – 73Combined sources4
Beta strandi76 – 81Combined sources6
Helixi86 – 88Combined sources3
Helixi91 – 94Combined sources4
Beta strandi97 – 101Combined sources5
Beta strandi103 – 105Combined sources3
Helixi109 – 112Combined sources4
Helixi114 – 117Combined sources4
Beta strandi121 – 127Combined sources7
Beta strandi130 – 132Combined sources3
Turni137 – 139Combined sources3
Helixi141 – 143Combined sources3
Beta strandi150 – 152Combined sources3
Helixi156 – 171Combined sources16
Beta strandi174 – 183Combined sources10
Beta strandi191 – 193Combined sources3
Helixi200 – 203Combined sources4
Helixi206 – 208Combined sources3
Beta strandi211 – 214Combined sources4
Helixi217 – 221Combined sources5
Turni222 – 224Combined sources3
Helixi226 – 228Combined sources3
Beta strandi231 – 238Combined sources8
Beta strandi245 – 255Combined sources11
Helixi259 – 271Combined sources13
Turni272 – 277Combined sources6
Beta strandi278 – 281Combined sources4
Helixi287 – 290Combined sources4
Beta strandi295 – 300Combined sources6
Turni301 – 303Combined sources3
Beta strandi305 – 308Combined sources4
Beta strandi311 – 318Combined sources8
Helixi322 – 335Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4Z0HX-ray2.30O/R5-338[»]
ProteinModelPortaliP25858.
SMRiP25858.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni155 – 157Glyceraldehyde 3-phosphate bindingBy similarity3
Regioni215 – 216Glyceraldehyde 3-phosphate bindingBy similarity2

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG0657. Eukaryota.
COG0057. LUCA.
HOGENOMiHOG000071678.
InParanoidiP25858.
KOiK00134.
OMAiIASEGTH.
OrthoDBiEOG09360F5Y.
PhylomeDBiP25858.

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]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01534. GAPDH-I. 1 hit.
PROSITEiPS00071. GAPDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P25858-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MADKKIRIGI NGFGRIGRLV ARVVLQRDDV ELVAVNDPFI TTEYMTYMFK
60 70 80 90 100
YDSVHGQWKH NELKIKDEKT LLFGEKPVTV FGIRNPEDIP WAEAGADYVV
110 120 130 140 150
ESTGVFTDKD KAAAHLKGGA KKVVISAPSK DAPMFVVGVN EHEYKSDLDI
160 170 180 190 200
VSNASCTTNC LAPLAKVIND RFGIVEGLMT TVHSITATQK TVDGPSMKDW
210 220 230 240 250
RGGRAASFNI IPSSTGAAKA VGKVLPALNG KLTGMSFRVP TVDVSVVDLT
260 270 280 290 300
VRLEKAATYD EIKKAIKEES EGKLKGILGY TEDDVVSTDF VGDNRSSIFD
310 320 330
AKAGIALSDK FVKLVSWYDN EWGYSSRVVD LIVHMSKA
Length:338
Mass (Da):36,914
Last modified:May 2, 2002 - v2
Checksum:i4186F65E1F1EE96F
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti127A → E in AAA32794 (PubMed:1916285).Curated1
Sequence conflicti127A → E in AAA32796 (PubMed:1916285).Curated1
Sequence conflicti136V → F in AAM65189 (Ref. 6) Curated1
Sequence conflicti260D → E in AAA32794 (PubMed:1916285).Curated1
Sequence conflicti260D → E in AAA32796 (PubMed:1916285).Curated1
Sequence conflicti325S → N in AAM65189 (Ref. 6) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M64116 mRNA. Translation: AAA32794.1.
M64119 Genomic DNA. Translation: AAA32796.1.
AC016829 Genomic DNA. Translation: AAF26801.1.
CP002686 Genomic DNA. Translation: AEE74039.1.
AY052267 mRNA. Translation: AAK97737.1.
AY060521 mRNA. Translation: AAL31134.1.
AY140084 mRNA. Translation: AAM98225.1.
AK226804 mRNA. Translation: BAE98901.1.
AY087651 mRNA. Translation: AAM65189.1.
F20074 mRNA. Translation: CAA23391.1.
PIRiJQ1287.
RefSeqiNP_187062.1. NM_111283.4.
UniGeneiAt.22963.
At.24406.
At.71328.

Genome annotation databases

EnsemblPlantsiAT3G04120.1; AT3G04120.1; AT3G04120.
GeneIDi819567.
GrameneiAT3G04120.1; AT3G04120.1; AT3G04120.
KEGGiath:AT3G04120.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M64116 mRNA. Translation: AAA32794.1.
M64119 Genomic DNA. Translation: AAA32796.1.
AC016829 Genomic DNA. Translation: AAF26801.1.
CP002686 Genomic DNA. Translation: AEE74039.1.
AY052267 mRNA. Translation: AAK97737.1.
AY060521 mRNA. Translation: AAL31134.1.
AY140084 mRNA. Translation: AAM98225.1.
AK226804 mRNA. Translation: BAE98901.1.
AY087651 mRNA. Translation: AAM65189.1.
F20074 mRNA. Translation: CAA23391.1.
PIRiJQ1287.
RefSeqiNP_187062.1. NM_111283.4.
UniGeneiAt.22963.
At.24406.
At.71328.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4Z0HX-ray2.30O/R5-338[»]
ProteinModelPortaliP25858.
SMRiP25858.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4902. 10 interactors.
IntActiP25858. 2 interactors.
MINTiMINT-8060263.
STRINGi3702.AT3G04120.1.

PTM databases

iPTMnetiP25858.

Proteomic databases

PaxDbiP25858.
PRIDEiP25858.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G04120.1; AT3G04120.1; AT3G04120.
GeneIDi819567.
GrameneiAT3G04120.1; AT3G04120.1; AT3G04120.
KEGGiath:AT3G04120.

Organism-specific databases

TAIRiAT3G04120.

Phylogenomic databases

eggNOGiKOG0657. Eukaryota.
COG0057. LUCA.
HOGENOMiHOG000071678.
InParanoidiP25858.
KOiK00134.
OMAiIASEGTH.
OrthoDBiEOG09360F5Y.
PhylomeDBiP25858.

Enzyme and pathway databases

UniPathwayiUPA00109; UER00184.
BRENDAi1.2.1.12. 399.
ReactomeiR-ATH-70171. Glycolysis.
R-ATH-70263. Gluconeogenesis.

Miscellaneous databases

PROiP25858.

Gene expression databases

GenevisibleiP25858. AT.

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]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01534. GAPDH-I. 1 hit.
PROSITEiPS00071. GAPDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiG3PC1_ARATH
AccessioniPrimary (citable) accession number: P25858
Secondary accession number(s): Q0WVE7
, Q42352, Q8LAS0, Q9M8W8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: May 2, 2002
Last modified: November 30, 2016
This is version 151 of the entry and version 2 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-dependent 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

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.