G3P_GEOSE
ID G3P_GEOSE Reviewed; 335 AA.
AC P00362;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 5.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=Glyceraldehyde-3-phosphate dehydrogenase {ECO:0000303|PubMed:7408868};
DE Short=GAPDH {ECO:0000303|PubMed:7408868};
DE EC=1.2.1.12 {ECO:0000250|UniProtKB:P09124};
DE AltName: Full=NAD-dependent glyceraldehyde-3-phosphate dehydrogenase {ECO:0000303|PubMed:7408868};
GN Name=gap;
OS Geobacillus stearothermophilus (Bacillus stearothermophilus).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus.
OX NCBI_TaxID=1422;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2684782; DOI=10.1016/0378-1119(89)90049-8;
RA Tesfay H.S., Amelunxen R.E., Goldberg I.D.;
RT "Nucleotide sequences of genes encoding heat-stable and heat-labile
RT glyceraldehyde-3-phosphate dehydrogenases; amino acid sequence and protein
RT thermostability.";
RL Gene 82:237-248(1989).
RN [2]
RP ERRATUM OF PUBMED:2684782, AND RETRACTION NOTICE OF PUBMED:2684782.
RX PubMed=2227448; DOI=10.1016/0378-1119(90)90484-9;
RA Tesfay H.S., Amelunxen R.E., Goldberg I.D.;
RL Gene 94:144-144(1990).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2656407; DOI=10.1016/0378-1119(89)90391-0;
RA Branlant C., Oster T., Branlant G.;
RT "Nucleotide sequence determination of the DNA region coding for Bacillus
RT stearothermophilus glyceraldehyde-3-phosphate dehydrogenase and of the
RT flanking DNA regions required for its expression in Escherichia coli.";
RL Gene 75:145-155(1989).
RN [4]
RP PROTEIN SEQUENCE OF 2-335.
RX PubMed=7408868; DOI=10.1111/j.1432-1033.1980.tb04751.x;
RA Walker J.E., Carne A.F., Runswick M.J., Bridgen J., Harris J.I.;
RT "D-glyceraldehyde-3-phosphate dehydrogenase. Complete amino-acid sequence
RT of the enzyme from Bacillus stearothermophilus.";
RL Eur. J. Biochem. 108:549-565(1980).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS), AND SUBUNIT.
RX PubMed=193030; DOI=10.1038/266328a0;
RA Biesecker G., Harris J.I., Thierry J.-C., Walker J.E., Wonacott A.J.;
RT "Sequence and structure of D-glyceraldehyde 3-phosphate dehydrogenase from
RT Bacillus stearothermophilus.";
RL Nature 266:328-333(1977).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH NAD AND SUBSTRATE
RP ANALOG, AND SUBUNIT.
RX PubMed=3586018; DOI=10.1016/0022-2836(87)90635-8;
RA Skarzynski T., Moody P.C.E., Wonacott A.J.;
RT "Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus
RT stearothermophilus at 1.8-A resolution.";
RL J. Mol. Biol. 193:171-187(1987).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) OF 2-335 IN COMPLEX WITH SUBSTRATE
RP ANALOG, AND SUBUNIT.
RX PubMed=3210237; DOI=10.1016/0022-2836(88)90130-1;
RA Skarzynski T., Wonacott A.J.;
RT "Coenzyme-induced conformational changes in glyceraldehyde-3-phosphate
RT dehydrogenase from Bacillus stearothermophilus.";
RL J. Mol. Biol. 203:1097-1118(1988).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) OF B-S AND D32G-S MUTANTS IN
RP COMPLEXES WITH NAD AND SUBSTRATE ANALOG, MUTAGENESIS OF 35-LEU--ASP-37;
RP CYS-152; LEU-190 AND PRO-191, AND SUBUNIT.
RX PubMed=9175858; DOI=10.1006/jmbi.1997.0998;
RA Didierjean C., Rahuel-Clermont S., Vitoux B., Dideberg O., Branlant G.,
RA Aubry A.;
RT "A crystallographic comparison between mutated glyceraldehyde-3-phosphate
RT dehydrogenases from Bacillus stearothermophilus complexed with either NAD+
RT or NADP+.";
RL J. Mol. Biol. 268:739-759(1997).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.11 ANGSTROMS) OF MUTANT ALA-152 IN COMPLEX WITH
RP NAD AND GLYCERALDEHYDE 3-PHOSPHATE, FUNCTION, MUTAGENESIS OF CYS-152,
RP REACTION MECHANISM, AND SUBUNIT.
RX PubMed=12569100; DOI=10.1074/jbc.m211040200;
RA Didierjean C., Corbier C., Fatih M., Favier F., Boschi-Muller S.,
RA Branlant G., Aubry A.;
RT "Crystal structure of two ternary complexes of phosphorylating
RT glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus
RT with NAD and D-glyceraldehyde 3-phosphate.";
RL J. Biol. Chem. 278:12968-12976(2003).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.77 ANGSTROMS) OF 2-335 IN COMPLEX WITH NAD AND
RP GLYCERALDEHYDE-3-PHOSPHATE, FUNCTION, ACTIVE SITE, REACTION MECHANISM, AND
RP SUBUNIT.
RX PubMed=18480053; DOI=10.1074/jbc.m802286200;
RA Moniot S., Bruno S., Vonrhein C., Didierjean C., Boschi-Muller S., Vas M.,
RA Bricogne G., Branlant G., Mozzarelli A., Corbier C.;
RT "Trapping of the thioacylglyceraldehyde-3-phosphate dehydrogenase
RT intermediate from Bacillus stearothermophilus. Direct evidence for a flip-
RT flop mechanism.";
RL J. Biol. Chem. 283:21693-21702(2008).
CC -!- FUNCTION: Catalyzes the oxidative phosphorylation of glyceraldehyde 3-
CC phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor
CC NAD. The first reaction step involves the formation of a hemiacetal
CC intermediate between G3P and a cysteine residue, and this hemiacetal
CC intermediate is then oxidized to a thioester, with concomitant
CC reduction of NAD to NADH. The reduced NADH is then exchanged with the
CC second NAD, and the thioester is attacked by a nucleophilic inorganic
CC phosphate to produce BPG. {ECO:0000269|PubMed:12569100,
CC ECO:0000269|PubMed:18480053}.
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:0000250|UniProtKB:P09124};
CC -!- PATHWAY: Carbohydrate degradation; glycolysis; pyruvate from D-
CC glyceraldehyde 3-phosphate: step 1/5. {ECO:0000305}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:12569100,
CC ECO:0000269|PubMed:18480053, ECO:0000269|PubMed:193030,
CC ECO:0000269|PubMed:3210237, ECO:0000269|PubMed:3586018,
CC ECO:0000269|PubMed:9175858}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305|PubMed:9175858}.
CC -!- SIMILARITY: Belongs to the glyceraldehyde-3-phosphate dehydrogenase
CC family. {ECO:0000305}.
CC -!- CAUTION: PubMed:2684782 sequence was incorrect and retracted in
CC PubMed:2227448. {ECO:0000305}.
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DR EMBL; M24493; AAA22461.1; -; Genomic_DNA.
DR PIR; JS0164; DEBSGF.
DR RefSeq; WP_033015082.1; NZ_RCTK01000017.1.
DR PDB; 1DBV; X-ray; 2.50 A; O/P/Q/R=2-335.
DR PDB; 1GD1; X-ray; 1.80 A; O/P/Q/R=2-335.
DR PDB; 1NPT; X-ray; 2.18 A; O/P/Q/R=2-335.
DR PDB; 1NQ5; X-ray; 2.11 A; A/C/O/Q=2-335.
DR PDB; 1NQA; X-ray; 2.20 A; O/P/Q/R=2-335.
DR PDB; 1NQO; X-ray; 2.01 A; A/C/O/Q=2-335.
DR PDB; 2DBV; X-ray; 2.20 A; O/P/Q/R=2-335.
DR PDB; 2GD1; X-ray; 2.50 A; O/P/Q/R=2-335.
DR PDB; 3CMC; X-ray; 1.77 A; O/P/Q/R=2-335.
DR PDB; 3DBV; X-ray; 2.45 A; O/P/Q/R=2-335.
DR PDB; 4DBV; X-ray; 2.50 A; O/P/Q/R=2-335.
DR PDBsum; 1DBV; -.
DR PDBsum; 1GD1; -.
DR PDBsum; 1NPT; -.
DR PDBsum; 1NQ5; -.
DR PDBsum; 1NQA; -.
DR PDBsum; 1NQO; -.
DR PDBsum; 2DBV; -.
DR PDBsum; 2GD1; -.
DR PDBsum; 3CMC; -.
DR PDBsum; 3DBV; -.
DR PDBsum; 4DBV; -.
DR AlphaFoldDB; P00362; -.
DR SMR; P00362; -.
DR DrugBank; DB02263; D-glyceraldehyde 3-phosphate.
DR PRIDE; P00362; -.
DR GeneID; 58573429; -.
DR BRENDA; 1.2.1.12; 623.
DR SABIO-RK; P00362; -.
DR UniPathway; UPA00109; UER00184.
DR EvolutionaryTrace; P00362; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004365; F:glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity; ISS:UniProtKB.
DR GO; GO:0051287; F:NAD binding; IDA:UniProtKB.
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; IEA:UniProtKB-UniPathway.
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; PTHR43148; PTHR43148; 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 Nucleotide-binding; Oxidoreductase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:7408868"
FT CHAIN 2..335
FT /note="Glyceraldehyde-3-phosphate dehydrogenase"
FT /id="PRO_0000145633"
FT ACT_SITE 152
FT /note="Nucleophile"
FT /evidence="ECO:0000269|PubMed:18480053,
FT ECO:0000305|PubMed:12569100"
FT BINDING 12..13
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:12569100,
FT ECO:0000269|PubMed:18480053, ECO:0000269|PubMed:3586018,
FT ECO:0000269|PubMed:9175858"
FT BINDING 34
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:12569100,
FT ECO:0000269|PubMed:18480053, ECO:0000269|PubMed:3586018,
FT ECO:0000269|PubMed:9175858"
FT BINDING 78
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:12569100,
FT ECO:0000269|PubMed:18480053, ECO:0000269|PubMed:3586018,
FT ECO:0000269|PubMed:9175858"
FT BINDING 120
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:12569100,
FT ECO:0000269|PubMed:18480053, ECO:0000269|PubMed:3586018,
FT ECO:0000269|PubMed:9175858"
FT BINDING 151..153
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000269|PubMed:12569100,
FT ECO:0000269|PubMed:18480053, ECO:0000269|PubMed:3210237,
FT ECO:0000269|PubMed:3586018, ECO:0000269|PubMed:9175858"
FT BINDING 182
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000269|PubMed:12569100,
FT ECO:0000269|PubMed:18480053, ECO:0000269|PubMed:3210237,
FT ECO:0000269|PubMed:3586018, ECO:0000269|PubMed:9175858"
FT BINDING 183
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:12569100,
FT ECO:0000269|PubMed:18480053, ECO:0000269|PubMed:3586018,
FT ECO:0000269|PubMed:9175858"
FT BINDING 197
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000269|PubMed:12569100,
FT ECO:0000269|PubMed:18480053, ECO:0000269|PubMed:9175858"
FT BINDING 210..211
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000269|PubMed:18480053,
FT ECO:0000269|PubMed:3210237, ECO:0000269|PubMed:3586018,
FT ECO:0000269|PubMed:9175858"
FT BINDING 233
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000269|PubMed:12569100,
FT ECO:0000269|PubMed:18480053, ECO:0000269|PubMed:3210237,
FT ECO:0000269|PubMed:3586018, ECO:0000269|PubMed:9175858"
FT BINDING 315
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:12569100,
FT ECO:0000269|PubMed:18480053, ECO:0000269|PubMed:3586018,
FT ECO:0000269|PubMed:9175858"
FT SITE 179
FT /note="Activates thiol group during catalysis"
FT /evidence="ECO:0000250|UniProtKB:Q6GIL8"
FT MUTAGEN 35..37
FT /note="LTD->TGG: In mutant B-S, the recognition of NAD is
FT slightly affected; when associated with A-190 and S-191."
FT /evidence="ECO:0000269|PubMed:9175858"
FT MUTAGEN 152
FT /note="C->A: Loss of dehydrogenase activity."
FT /evidence="ECO:0000269|PubMed:12569100,
FT ECO:0000269|PubMed:9175858"
FT MUTAGEN 152
FT /note="C->S: Possesses a low residual dehydrogenase
FT activity."
FT /evidence="ECO:0000269|PubMed:12569100"
FT MUTAGEN 190
FT /note="L->A: In mutant D32G-S, a strong alteration of the
FT affinity for NAD is observed; when associated with S-191.
FT In mutant B-S, the recognition of NAD is slightly affected;
FT when associated with 35-T--G-37 and S-191."
FT /evidence="ECO:0000269|PubMed:9175858"
FT MUTAGEN 191
FT /note="P->S: In mutant D32G-S, a strong alteration of the
FT affinity for NAD is observed; when associated with A-190.
FT In mutant B-S, the recognition of NAD is slightly affected;
FT when associated with 35-T--G-37 and A-190."
FT /evidence="ECO:0000269|PubMed:9175858"
FT STRAND 3..9
FT /evidence="ECO:0007829|PDB:3CMC"
FT HELIX 12..21
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 27..33
FT /evidence="ECO:0007829|PDB:3CMC"
FT HELIX 38..46
FT /evidence="ECO:0007829|PDB:3CMC"
FT TURN 49..51
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 58..61
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 64..67
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 70..75
FT /evidence="ECO:0007829|PDB:3CMC"
FT HELIX 80..82
FT /evidence="ECO:0007829|PDB:3CMC"
FT HELIX 86..88
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 92..95
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 97..99
FT /evidence="ECO:0007829|PDB:3CMC"
FT HELIX 103..106
FT /evidence="ECO:0007829|PDB:3CMC"
FT HELIX 108..111
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 115..121
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 127..129
FT /evidence="ECO:0007829|PDB:3CMC"
FT TURN 132..134
FT /evidence="ECO:0007829|PDB:3CMC"
FT HELIX 136..138
FT /evidence="ECO:0007829|PDB:3CMC"
FT TURN 141..143
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 146..148
FT /evidence="ECO:0007829|PDB:3CMC"
FT HELIX 152..168
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 170..180
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 185..189
FT /evidence="ECO:0007829|PDB:3CMC"
FT TURN 195..198
FT /evidence="ECO:0007829|PDB:3CMC"
FT TURN 201..203
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 206..209
FT /evidence="ECO:0007829|PDB:3CMC"
FT HELIX 212..219
FT /evidence="ECO:0007829|PDB:3CMC"
FT HELIX 221..223
FT /evidence="ECO:0007829|PDB:3CMC"
FT TURN 224..226
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 227..235
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 240..250
FT /evidence="ECO:0007829|PDB:3CMC"
FT HELIX 254..266
FT /evidence="ECO:0007829|PDB:3CMC"
FT TURN 267..272
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 273..276
FT /evidence="ECO:0007829|PDB:3CMC"
FT HELIX 282..285
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 290..295
FT /evidence="ECO:0007829|PDB:3CMC"
FT HELIX 296..298
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 300..302
FT /evidence="ECO:0007829|PDB:3CMC"
FT TURN 303..305
FT /evidence="ECO:0007829|PDB:3CMC"
FT STRAND 306..313
FT /evidence="ECO:0007829|PDB:3CMC"
FT HELIX 317..332
FT /evidence="ECO:0007829|PDB:3CMC"
SQ SEQUENCE 335 AA; 36075 MW; DBAAA2DD24497E18 CRC64;
MAVKVGINGF GRIGRNVFRA ALKNPDIEVV AVNDLTDANT LAHLLKYDSV HGRLDAEVSV
NGNNLVVNGK EIIVKAERDP ENLAWGEIGV DIVVESTGRF TKREDAAKHL EAGAKKVIIS
APAKNEDITI VMGVNQDKYD PKAHHVISNA SCTTNCLAPF AKVLHEQFGI VRGMMTTVHS
YTNDQRILDL PHKDLRRARA AAESIIPTTT GAAKAVALVL PELKGKLNGM AMRVPTPNVS
VVDLVAELEK EVTVEEVNAA LKAAAEGELK GILAYSEEPL VSRDYNGSTV SSTIDALSTM
VIDGKMVKVV SWYDNETGYS HRVVDLAAYI ASKGL
