2G82 | pdb_00002g82

High Resolution Structures of Thermus aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role of 220's Loop Motion in Catalysis

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H [auth D]	d2g82d1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
H [auth D]	d2g82d2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
G [auth C]	d2g82c1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
G [auth C]	d2g82c2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
F [auth B]	d2g82b1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
F [auth B]	d2g82b2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
E [auth A]	d2g82a1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
E [auth A]	d2g82a2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
D [auth R]	d2g82r1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
D [auth R]	d2g82r2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
C [auth Q]	d2g82q1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
C [auth Q]	d2g82q2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
B [auth P]	d2g82p1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
B [auth P]	d2g82p2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
A [auth O]	d2g82o1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
A [auth O]	d2g82o2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H [auth D]	SCOP2B Superfamily	GAPDH-like	8056116	3000043	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	GAPDH-like	8056116	3000043	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	GAPDH-like	8056116	3000043	SCOP2B (2022-06-29)
E [auth A]	SCOP2 Family	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like	8056115	4000077	SCOP2 (2022-06-29)
E [auth A]	SCOP2 Superfamily	GAPDH-like	8056116	3000043	SCOP2 (2022-06-29)
D [auth R]	SCOP2B Superfamily	GAPDH-like	8056116	3000043	SCOP2B (2022-06-29)
C [auth Q]	SCOP2B Superfamily	GAPDH-like	8056116	3000043	SCOP2B (2022-06-29)
B [auth P]	SCOP2B Superfamily	GAPDH-like	8056116	3000043	SCOP2B (2022-06-29)
A [auth O]	SCOP2B Superfamily	GAPDH-like	8056116	3000043	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H [auth D]	YceM-like_C	e2g82D1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.1)
H [auth D]	NAD_binding_3	e2g82D2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (v294.1)
G [auth C]	YceM-like_C	e2g82C1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.1)
G [auth C]	NAD_binding_3	e2g82C2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (v294.1)
F [auth B]	YceM-like_C	e2g82B1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.1)
F [auth B]	NAD_binding_3	e2g82B2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (v294.1)
E [auth A]	Gp_dh_C	e2g82A1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: Gp_dh_C	ECOD (v294.1)
E [auth A]	Gp_dh_N	e2g82A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Gp_dh_N	ECOD (v294.1)
D [auth R]	YceM-like_C	e2g82R1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.1)
D [auth R]	NAD_binding_3	e2g82R2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (v294.1)
C [auth Q]	YceM-like_C	e2g82Q1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.1)
C [auth Q]	NAD_binding_3	e2g82Q2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (v294.1)
B [auth P]	YceM-like_C	e2g82P1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.1)
B [auth P]	NAD_binding_3	e2g82P2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (v294.1)
A [auth O]	YceM-like_C	e2g82O1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.1)
A [auth O]	NAD_binding_3	e2g82O2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth D]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H [auth D]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
G [auth C]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G [auth C]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
F [auth B]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F [auth B]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
E [auth A]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E [auth A]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
D [auth R]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D [auth R]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
C [auth Q]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C [auth Q]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
B [auth P]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B [auth P]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
A [auth O]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A [auth O]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], F [auth B], G [auth C], H [auth D]	Glyceraldehyde-3-phosphate dehydrogenase	binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity oxidoreductase activity glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] (phosphorylating) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity oxidoreductase activity glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] (phosphorylating) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor NAD binding	ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process nucleobase-containing compound metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process nucleobase-containing compound metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process purine nucleoside diphosphate metabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration catabolic process ATP metabolic process energy derivation by oxidation of organic compounds purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process cellular process purine ribonucleoside diphosphate catabolic process monosaccharide metabolic process hexose metabolic process glucose metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], F [auth B], G [auth C], H [auth D]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], F [auth B], G [auth C], H [auth D]	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family	Family
A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], F [auth B], G [auth C], H [auth D]	IPR020829	Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain	Domain
A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], F [auth B], G [auth C], H [auth D]	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain	Domain
A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], F [auth B], G [auth C], H [auth D]	IPR020830	Glyceraldehyde 3-phosphate dehydrogenase, active site	Active Site
A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], F [auth B], G [auth C], H [auth D]	IPR006424	Glyceraldehyde-3-phosphate dehydrogenase, type I	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], F [auth B], G [auth C], H [auth D]	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.