G3P1_STAAR
ID G3P1_STAAR Reviewed; 336 AA.
AC Q6GIL8;
DT 01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=Glyceraldehyde-3-phosphate dehydrogenase 1 {ECO:0000303|PubMed:20620151};
DE Short=GAPDH 1 {ECO:0000303|PubMed:20620151};
DE EC=1.2.1.12 {ECO:0000269|PubMed:20620151};
DE AltName: Full=NAD-dependent glyceraldehyde-3-phosphate dehydrogenase {ECO:0000303|PubMed:20620151};
GN Name=gapA1; Synonyms=gap, gapA; OrderedLocusNames=SAR0828;
OS Staphylococcus aureus (strain MRSA252).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=282458;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MRSA252;
RX PubMed=15213324; DOI=10.1073/pnas.0402521101;
RA Holden M.T.G., Feil E.J., Lindsay J.A., Peacock S.J., Day N.P.J.,
RA Enright M.C., Foster T.J., Moore C.E., Hurst L., Atkin R., Barron A.,
RA Bason N., Bentley S.D., Chillingworth C., Chillingworth T., Churcher C.,
RA Clark L., Corton C., Cronin A., Doggett J., Dowd L., Feltwell T., Hance Z.,
RA Harris B., Hauser H., Holroyd S., Jagels K., James K.D., Lennard N.,
RA Line A., Mayes R., Moule S., Mungall K., Ormond D., Quail M.A.,
RA Rabbinowitsch E., Rutherford K.M., Sanders M., Sharp S., Simmonds M.,
RA Stevens K., Whitehead S., Barrell B.G., Spratt B.G., Parkhill J.;
RT "Complete genomes of two clinical Staphylococcus aureus strains: evidence
RT for the rapid evolution of virulence and drug resistance.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:9786-9791(2004).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF MUTANT SER-151 IN COMPLEX WITH
RP GLYCERALDEHYDE-3-PHOSPHATE AND NAD, FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF CYS-151 AND HIS-178, ACTIVE
RP SITE, AND SUBUNIT.
RC STRAIN=MRSA252;
RX PubMed=20620151; DOI=10.1016/j.jmb.2010.07.002;
RA Mukherjee S., Dutta D., Saha B., Das A.K.;
RT "Crystal structure of glyceraldehyde-3-phosphate dehydrogenase 1 from
RT methicillin-resistant Staphylococcus aureus MRSA252 provides novel insights
RT into substrate binding and catalytic mechanism.";
RL J. Mol. Biol. 401:949-968(2010).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (3.19 ANGSTROMS) IN COMPLEX WITH NAD, AND SUBUNIT.
RC STRAIN=MRSA252;
RA Roychowdhury A., Mukherjee S., Dutta D., Das A.K.;
RT "Crystal structure of Staphylococcal GAPDH1 in a hexagonal space group.";
RL Submitted (DEC-2011) to the PDB data bank.
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:20620151}.
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:0000269|PubMed:20620151};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.31 mM for G3P {ECO:0000269|PubMed:20620151};
CC KM=316 mM for NAD {ECO:0000269|PubMed:20620151};
CC Note=kcat is 70 sec(-1) for dehydrogenase activity.
CC {ECO:0000269|PubMed:20620151};
CC pH dependence:
CC Optimum pH is 8.7. {ECO:0000269|PubMed:20620151};
CC Temperature dependence:
CC Optimum temperature is 25 degrees Celsius.
CC {ECO:0000269|PubMed:20620151};
CC -!- PATHWAY: Carbohydrate degradation; glycolysis; pyruvate from D-
CC glyceraldehyde 3-phosphate: step 1/5. {ECO:0000305|PubMed:20620151}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:20620151,
CC ECO:0000269|Ref.3}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the glyceraldehyde-3-phosphate dehydrogenase
CC family. {ECO:0000305}.
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DR EMBL; BX571856; CAG39837.1; -; Genomic_DNA.
DR RefSeq; WP_000279414.1; NC_002952.2.
DR PDB; 3HQ4; X-ray; 2.20 A; O/P/Q/R=1-336.
DR PDB; 3K73; X-ray; 2.50 A; O/P/Q/R=1-336.
DR PDB; 3K9Q; X-ray; 2.50 A; O/P/Q/R=1-336.
DR PDB; 3KSD; X-ray; 2.20 A; O/P/Q/R=1-336.
DR PDB; 3KSZ; X-ray; 2.60 A; O/P/Q/R=1-336.
DR PDB; 3KV3; X-ray; 2.50 A; O/P/Q/R=1-336.
DR PDB; 3L4S; X-ray; 2.20 A; O/P/Q/R=1-336.
DR PDB; 3L6O; X-ray; 2.20 A; O/P/Q/R=1-336.
DR PDB; 3LC1; X-ray; 2.00 A; O/P/Q/R=1-336.
DR PDB; 3LC2; X-ray; 2.80 A; O/P/Q/R=1-336.
DR PDB; 3LC7; X-ray; 2.50 A; O/P/Q/R=1-336.
DR PDB; 3LVF; X-ray; 1.70 A; O/P/Q/R=1-336.
DR PDB; 3VAZ; X-ray; 3.19 A; A/B/O/P/Q/R=1-336.
DR PDB; 5T73; X-ray; 2.60 A; A/B/C/D=1-336.
DR PDBsum; 3HQ4; -.
DR PDBsum; 3K73; -.
DR PDBsum; 3K9Q; -.
DR PDBsum; 3KSD; -.
DR PDBsum; 3KSZ; -.
DR PDBsum; 3KV3; -.
DR PDBsum; 3L4S; -.
DR PDBsum; 3L6O; -.
DR PDBsum; 3LC1; -.
DR PDBsum; 3LC2; -.
DR PDBsum; 3LC7; -.
DR PDBsum; 3LVF; -.
DR PDBsum; 3VAZ; -.
DR PDBsum; 5T73; -.
DR AlphaFoldDB; Q6GIL8; -.
DR SMR; Q6GIL8; -.
DR MoonProt; Q6GIL8; -.
DR KEGG; sar:SAR0828; -.
DR HOGENOM; CLU_030140_0_0_9; -.
DR OMA; NCVAPMA; -.
DR OrthoDB; 944149at2; -.
DR BRENDA; 1.2.1.12; 3352.
DR UniPathway; UPA00109; UER00184.
DR EvolutionaryTrace; Q6GIL8; -.
DR Proteomes; UP000000596; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004365; F:glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity; IDA: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; Glycolysis; NAD; Nucleotide-binding;
KW Oxidoreductase.
FT CHAIN 1..336
FT /note="Glyceraldehyde-3-phosphate dehydrogenase 1"
FT /id="PRO_0000145685"
FT ACT_SITE 151
FT /note="Nucleophile"
FT /evidence="ECO:0000269|PubMed:20620151"
FT BINDING 12..13
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:20620151, ECO:0000269|Ref.3"
FT BINDING 34
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:20620151, ECO:0000269|Ref.3"
FT BINDING 120
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:20620151, ECO:0000269|Ref.3"
FT BINDING 150..152
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000269|PubMed:20620151"
FT BINDING 181
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000269|PubMed:20620151"
FT BINDING 198
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000250|UniProtKB:P00362"
FT BINDING 211..212
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000269|PubMed:20620151"
FT BINDING 234
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000269|PubMed:20620151"
FT BINDING 316
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:20620151"
FT SITE 178
FT /note="Activates thiol group during catalysis"
FT /evidence="ECO:0000269|PubMed:20620151"
FT MUTAGEN 151
FT /note="C->S: Loss of dehydrogenase activity."
FT /evidence="ECO:0000269|PubMed:20620151"
FT MUTAGEN 178
FT /note="H->N: Loss of dehydrogenase activity."
FT /evidence="ECO:0000269|PubMed:20620151"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:3LVF"
FT HELIX 12..22
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 27..33
FT /evidence="ECO:0007829|PDB:3LVF"
FT HELIX 38..46
FT /evidence="ECO:0007829|PDB:3LVF"
FT TURN 49..51
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 58..61
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 64..67
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 70..75
FT /evidence="ECO:0007829|PDB:3LVF"
FT HELIX 80..82
FT /evidence="ECO:0007829|PDB:3LVF"
FT TURN 85..89
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 91..95
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 97..99
FT /evidence="ECO:0007829|PDB:3LVF"
FT HELIX 103..111
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 115..121
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 124..126
FT /evidence="ECO:0007829|PDB:3LVF"
FT TURN 132..134
FT /evidence="ECO:0007829|PDB:3LVF"
FT HELIX 136..138
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 144..147
FT /evidence="ECO:0007829|PDB:3LVF"
FT HELIX 151..167
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 169..179
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 186..188
FT /evidence="ECO:0007829|PDB:3LVF"
FT TURN 196..199
FT /evidence="ECO:0007829|PDB:3LVF"
FT HELIX 202..204
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 207..210
FT /evidence="ECO:0007829|PDB:3LVF"
FT TURN 213..216
FT /evidence="ECO:0007829|PDB:3LVF"
FT HELIX 217..219
FT /evidence="ECO:0007829|PDB:3LVF"
FT HELIX 222..224
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 227..236
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 241..253
FT /evidence="ECO:0007829|PDB:3LVF"
FT HELIX 256..265
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 269..274
FT /evidence="ECO:0007829|PDB:3LVF"
FT HELIX 280..283
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 289..293
FT /evidence="ECO:0007829|PDB:3LVF"
FT HELIX 294..296
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 298..302
FT /evidence="ECO:0007829|PDB:3LVF"
FT STRAND 305..314
FT /evidence="ECO:0007829|PDB:3LVF"
FT HELIX 318..334
FT /evidence="ECO:0007829|PDB:3LVF"
SQ SEQUENCE 336 AA; 36281 MW; 37A6CEA9376779E5 CRC64;
MAVKVAINGF GRIGRLAFRR IQEVEGLEVV AVNDLTDDDM LAHLLKYDTM QGRFTGEVEV
VDGGFRVNGK EVKSFSEPDA SKLPWKDLNI DVVLECTGFY TDKDKAQAHI EAGAKKVLIS
APATGDLKTI VFNTNHQELD GSETVVSGAS CTTNSLAPVA KVLNDDFGLV EGLMTTIHAY
TGDQNTQDAP HRKGDKRRAR AAAENIIPNS TGAAKAIGKV IPEIDGKLDG GAQRVPVATG
SLTELTVVLE KQDVTVEQVN EAMKNASNES FGYTEDEIVS SDVVGMTYGS LFDATQTRVM
SVGDRQLVKV AAWYDNEMSY TAQLVRTLAY LAELSK
