G3PC1_ORYSJ
ID G3PC1_ORYSJ Reviewed; 337 AA.
AC Q0J8A4; B7EIW3; Q42977; Q6ZK60;
DT 10-JUL-2007, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic;
DE EC=1.2.1.12;
DE AltName: Full=PP38;
GN Name=GAPC1; Synonyms=GAPC, GAPDH, GPC;
GN OrderedLocusNames=Os08g0126300, LOC_Os08g03290;
GN ORFNames=OJ1163_G08.15, OsJ_024858;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Ilpoombyeo; TISSUE=Seed;
RA Yoon U.H., Kim Y.H.;
RT "Structural and expression analysis of germinating seed genes in Oryza
RT sativa L.";
RL Submitted (AUG-2009) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [7]
RP PROTEIN SEQUENCE OF 2-11; 30-39 AND 140-149.
RC STRAIN=cv. Nipponbare; TISSUE=Anther, Callus, Embryo, Panicle, and Stem;
RX PubMed=14681440; DOI=10.1093/nar/gkh020;
RA Komatsu S., Kojima K., Suzuki K., Ozaki K., Higo K.;
RT "Rice proteome database based on two-dimensional polyacrylamide gel
RT electrophoresis: its status in 2003.";
RL Nucleic Acids Res. 32:D388-D392(2004).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY, INDUCTION, AND PHOSPHORYLATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=16028114; DOI=10.1007/s11103-005-4013-1;
RA Khan M.M.K., Jan A., Karibe H., Komatsu S.;
RT "Identification of phosphoproteins regulated by gibberellin in rice leaf
RT sheath.";
RL Plant Mol. Biol. 58:27-40(2005).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEX WITH NAD, SUBUNIT,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF PHE-37.
RX PubMed=22903596; DOI=10.1007/s11103-012-9953-7;
RA Tien Y.C., Chuankhayan P., Huang Y.C., Chen C.D., Alikhajeh J., Chang S.L.,
RA Chen C.J.;
RT "Crystal structures of rice (Oryza sativa) glyceraldehyde-3-phosphate
RT dehydrogenase complexes with NAD and sulfate suggest involvement of Phe37
RT in NAD binding for catalysis.";
RL Plant Mol. Biol. 80:389-403(2012).
CC -!- FUNCTION: Key enzyme in glycolysis that catalyzes the first step of the
CC pathway by converting D-glyceraldehyde 3-phosphate (G3P) into 3-
CC phospho-D-glyceroyl phosphate. Essential for the maintenance of
CC cellular ATP levels and carbohydrate metabolism (By similarity).
CC {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-glyceraldehyde 3-phosphate + NAD(+) + phosphate = (2R)-3-
CC phospho-glyceroyl phosphate + H(+) + NADH; Xref=Rhea:RHEA:10300,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:43474, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57604, ChEBI:CHEBI:57945, ChEBI:CHEBI:59776; EC=1.2.1.12;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU10009};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.061 mM for NADH {ECO:0000269|PubMed:22903596};
CC KM=0.059 mM for NAD(+) {ECO:0000269|PubMed:22903596};
CC KM=0.036 mM for 3-phospho-D-glyceroyl phosphate
CC {ECO:0000269|PubMed:22903596};
CC KM=0.111 mM for D-glyceraldehyde 3-phosphate
CC {ECO:0000269|PubMed:22903596};
CC -!- PATHWAY: Carbohydrate degradation; glycolysis; pyruvate from D-
CC glyceraldehyde 3-phosphate: step 1/5.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:22903596}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- INDUCTION: By gibberellin. {ECO:0000269|PubMed:16028114}.
CC -!- PTM: Phosphorylated after gibberellin treatment.
CC {ECO:0000269|PubMed:16028114}.
CC -!- MISCELLANEOUS: Plants contain two types of GAPDH: cytosolic forms which
CC participate in glycolysis and chloroplast forms which participate in
CC photosynthesis. All the forms are encoded by distinct genes.
CC -!- SIMILARITY: Belongs to the glyceraldehyde-3-phosphate dehydrogenase
CC family. {ECO:0000305}.
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DR EMBL; EF122472; ABL74559.1; -; mRNA.
DR EMBL; GQ848031; ADM86844.1; -; mRNA.
DR EMBL; AP003886; BAD08850.1; -; Genomic_DNA.
DR EMBL; AP008214; BAF22811.1; -; Genomic_DNA.
DR EMBL; AP014964; BAT03659.1; -; Genomic_DNA.
DR EMBL; CM000145; EAZ41375.1; -; Genomic_DNA.
DR EMBL; AK071097; BAG92310.1; -; mRNA.
DR EMBL; AK103777; BAG96258.1; -; mRNA.
DR RefSeq; XP_015650130.1; XM_015794644.1.
DR PDB; 3E5R; X-ray; 2.30 A; A/B/C/O=1-337.
DR PDB; 3E6A; X-ray; 3.77 A; A/B/C/O=2-337.
DR PDB; 3V1Y; X-ray; 1.86 A; A/B/C/O=1-337.
DR PDBsum; 3E5R; -.
DR PDBsum; 3E6A; -.
DR PDBsum; 3V1Y; -.
DR AlphaFoldDB; Q0J8A4; -.
DR SMR; Q0J8A4; -.
DR BioGRID; 813601; 1.
DR STRING; 4530.OS08T0126300-01; -.
DR PaxDb; Q0J8A4; -.
DR PRIDE; Q0J8A4; -.
DR EnsemblPlants; Os08t0126300-01; Os08t0126300-01; Os08g0126300.
DR EnsemblPlants; Os08t0126300-02; Os08t0126300-02; Os08g0126300.
DR GeneID; 4344564; -.
DR Gramene; Os08t0126300-01; Os08t0126300-01; Os08g0126300.
DR Gramene; Os08t0126300-02; Os08t0126300-02; Os08g0126300.
DR KEGG; osa:4344564; -.
DR eggNOG; KOG0657; Eukaryota.
DR HOGENOM; CLU_030140_0_3_1; -.
DR InParanoid; Q0J8A4; -.
DR OMA; QCIVEST; -.
DR OrthoDB; 945145at2759; -.
DR BRENDA; 1.2.1.12; 4460.
DR PlantReactome; R-OSA-1119273; Lysine biosynthesis I.
DR PlantReactome; R-OSA-1119283; Lysine biosynthesis II.
DR PlantReactome; R-OSA-1119570; Cytosolic glycolysis.
DR SABIO-RK; Q0J8A4; -.
DR UniPathway; UPA00109; UER00184.
DR EvolutionaryTrace; Q0J8A4; -.
DR Proteomes; UP000000763; Chromosome 8.
DR Proteomes; UP000007752; Chromosome 8.
DR Proteomes; UP000059680; Chromosome 8.
DR ExpressionAtlas; Q0J8A4; baseline and differential.
DR Genevisible; Q0J8A4; OS.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0004365; F:glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity; IBA:GO_Central.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0050661; F:NADP binding; IEA:InterPro.
DR GO; GO:0006006; P:glucose metabolic process; IEA:InterPro.
DR GO; GO:0006096; P:glycolytic process; IBA:GO_Central.
DR InterPro; IPR020831; GlycerAld/Erythrose_P_DH.
DR InterPro; IPR020830; GlycerAld_3-P_DH_AS.
DR InterPro; IPR020829; GlycerAld_3-P_DH_cat.
DR InterPro; IPR020828; GlycerAld_3-P_DH_NAD(P)-bd.
DR InterPro; IPR006424; Glyceraldehyde-3-P_DH_1.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR PANTHER; PTHR10836; PTHR10836; 1.
DR Pfam; PF02800; Gp_dh_C; 1.
DR Pfam; PF00044; Gp_dh_N; 1.
DR PIRSF; PIRSF000149; GAP_DH; 1.
DR PRINTS; PR00078; G3PDHDRGNASE.
DR SMART; SM00846; Gp_dh_N; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR01534; GAPDH-I; 1.
DR PROSITE; PS00071; GAPDH; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Glycolysis; NAD;
KW Oxidoreductase; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:14681440"
FT CHAIN 2..337
FT /note="Glyceraldehyde-3-phosphate dehydrogenase 1,
FT cytosolic"
FT /id="PRO_0000145609"
FT ACT_SITE 154
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10009"
FT BINDING 13..14
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:22903596"
FT BINDING 35
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:22903596"
FT BINDING 82
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:22903596"
FT BINDING 153..155
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000250"
FT BINDING 184
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000250"
FT BINDING 213..214
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000250"
FT BINDING 236
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000250"
FT BINDING 318
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT SITE 181
FT /note="Activates thiol group during catalysis"
FT /evidence="ECO:0000250"
FT MUTAGEN 37
FT /note="F->G,T: 7-fold decrease in affinity toward NAD. More
FT than 500-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:22903596"
FT MUTAGEN 37
FT /note="F->L: 9-fold decrease in affinity toward NAD. More
FT than 1000-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:22903596"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:3V1Y"
FT HELIX 13..23
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 26..34
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 36..38
FT /evidence="ECO:0007829|PDB:3E5R"
FT HELIX 40..48
FT /evidence="ECO:0007829|PDB:3V1Y"
FT TURN 51..53
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 61..65
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 68..71
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 74..79
FT /evidence="ECO:0007829|PDB:3V1Y"
FT HELIX 84..86
FT /evidence="ECO:0007829|PDB:3V1Y"
FT HELIX 89..92
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 101..103
FT /evidence="ECO:0007829|PDB:3V1Y"
FT HELIX 107..110
FT /evidence="ECO:0007829|PDB:3V1Y"
FT HELIX 112..115
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 120..125
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 128..130
FT /evidence="ECO:0007829|PDB:3V1Y"
FT TURN 135..137
FT /evidence="ECO:0007829|PDB:3V1Y"
FT HELIX 139..141
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:3V1Y"
FT HELIX 154..170
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 172..181
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 187..191
FT /evidence="ECO:0007829|PDB:3V1Y"
FT HELIX 198..201
FT /evidence="ECO:0007829|PDB:3V1Y"
FT HELIX 204..206
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 209..212
FT /evidence="ECO:0007829|PDB:3V1Y"
FT HELIX 215..222
FT /evidence="ECO:0007829|PDB:3V1Y"
FT HELIX 224..226
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 229..236
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 243..253
FT /evidence="ECO:0007829|PDB:3V1Y"
FT HELIX 257..269
FT /evidence="ECO:0007829|PDB:3V1Y"
FT TURN 270..272
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 276..279
FT /evidence="ECO:0007829|PDB:3V1Y"
FT HELIX 285..288
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 294..298
FT /evidence="ECO:0007829|PDB:3V1Y"
FT TURN 299..301
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 303..306
FT /evidence="ECO:0007829|PDB:3V1Y"
FT STRAND 309..316
FT /evidence="ECO:0007829|PDB:3V1Y"
FT HELIX 320..335
FT /evidence="ECO:0007829|PDB:3V1Y"
SQ SEQUENCE 337 AA; 36413 MW; 3A8154CF7A06A603 CRC64;
MGKIKIGING FGRIGRLVAR VALQSEDVEL VAVNDPFITT DYMTYMFKYD TVHGQWKHSD
IKIKDSKTLL LGEKPVTVFG IRNPDEIPWA EAGAEYVVES TGVFTDKEKA AAHLKGGAKK
VVISAPSKDA PMFVCGVNED KYTSDIDIVS NASCTTNCLA PLAKVIHDNF GIIEGLMTTV
HAITATQKTV DGPSSKDWRG GRAASFNIIP SSTGAAKAVG KVLPDLNGKL TGMSFRVPTV
DVSVVDLTVR IEKAASYDAI KSAIKSASEG KLKGIIGYVE EDLVSTDFVG DSRSSIFDAK
AGIALNDNFV KLVAWYDNEW GYSNRVIDLI RHMAKTQ
