1CF2

THREE-DIMENSIONAL STRUCTURE OF D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM THE HYPERTHERMOPHILIC ARCHAEON METHANOTHERMUS FERVIDUS

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth P]	d1cf2p1	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)	(Methanothermus fervidus ) [TaxId: 2180 ],	SCOPe (2.08)
A [auth P]	d1cf2p2	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)	(Methanothermus fervidus ) [TaxId: 2180 ],	SCOPe (2.08)
B [auth R]	d1cf2r1	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)	(Methanothermus fervidus ) [TaxId: 2180 ],	SCOPe (2.08)
B [auth R]	d1cf2r2	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)	(Methanothermus fervidus ) [TaxId: 2180 ],	SCOPe (2.08)
C [auth O]	d1cf2o1	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)	(Methanothermus fervidus ) [TaxId: 2180 ],	SCOPe (2.08)
C [auth O]	d1cf2o2	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)	(Methanothermus fervidus ) [TaxId: 2180 ],	SCOPe (2.08)
D [auth Q]	d1cf2q1	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)	(Methanothermus fervidus ) [TaxId: 2180 ],	SCOPe (2.08)
D [auth Q]	d1cf2q2	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)	(Methanothermus fervidus ) [TaxId: 2180 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth P]	SCOP2B Superfamily	GAPDH-like	8056122	3000043	SCOP2B (2022-06-29)
B [auth R]	SCOP2B Superfamily	GAPDH-like	8056122	3000043	SCOP2B (2022-06-29)
C [auth O]	SCOP2 Family	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like	8056121	4000077	SCOP2 (2022-06-29)
C [auth O]	SCOP2 Superfamily	GAPDH-like	8056122	3000043	SCOP2 (2022-06-29)
D [auth Q]	SCOP2B Superfamily	GAPDH-like	8056122	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)
A [auth P]	Gp_dh_C_1	e1cf2P1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: Gp_dh_C_1	ECOD (1.6)
A [auth P]	DapB_N	e1cf2P2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DapB_N	ECOD (1.6)
B [auth R]	Gp_dh_C_1	e1cf2R1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: Gp_dh_C_1	ECOD (1.6)
B [auth R]	DapB_N	e1cf2R2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DapB_N	ECOD (1.6)
C [auth O]	Gp_dh_C_1	e1cf2O1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: Gp_dh_C_1	ECOD (1.6)
C [auth O]	DapB_N	e1cf2O2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DapB_N	ECOD (1.6)
D [auth Q]	Gp_dh_C_1	e1cf2Q1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: Gp_dh_C_1	ECOD (1.6)
D [auth Q]	DapB_N	e1cf2Q2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DapB_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth P], B [auth R], C [auth O], D [auth Q]	PF02800	Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain (Gp_dh_C)	Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain	GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. C-terminal domain is a mixed alpha/antiparallel beta fold.	Domain
A [auth P], B [auth R], C [auth O], D [auth Q]	PF01113	Dihydrodipicolinate reductase, N-terminus (DapB_N)	Dihydrodipicolinate reductase, N-terminus	Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for b ...	Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth P], B [auth R], C [auth O], D [auth Q]	PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)	binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding oxidoreductase activity glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] (phosphorylating) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding oxidoreductase activity glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) 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 oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-CH group of donors 4-hydroxy-tetrahydrodipicolinate reductase glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity NAD binding	ribonucleotide catabolic process pyridine nucleotide catabolic process 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 ribonucleotide catabolic process pyridine nucleotide catabolic process 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 pyridine nucleotide 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 catabolic process ATP metabolic process 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 ribonucleoside triphosphate metabolic 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 lysine metabolic process aspartate family amino acid biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process lysine biosynthetic process small molecule biosynthetic process dicarboxylic acid metabolic process L-amino acid biosynthetic process L-amino acid metabolic process diaminopimelate metabolic process fatty acid derivative metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process lysine biosynthetic process via diaminopimelate proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process lipid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth P], B [auth R], C [auth O], D [auth Q]	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain	Domain
A [auth P], B [auth R], C [auth O], D [auth Q]	IPR020830	Glyceraldehyde 3-phosphate dehydrogenase, active site	Active Site
A [auth P], B [auth R], C [auth O], D [auth Q]	IPR000846	Dihydrodipicolinate reductase, N-terminal	Domain
A [auth P], B [auth R], C [auth O], D [auth Q]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A [auth P], B [auth R], C [auth O], D [auth Q]	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family	Family
A [auth P], B [auth R], C [auth O], D [auth Q]	IPR020829	Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain	Domain
A [auth P], B [auth R], C [auth O], D [auth Q]	IPR006436	Glyceraldehyde-3-phosphate dehydrogenase, type II	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A [auth P]	glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) M-CSA #619	Archaebacterial glyceraldehyde-3-phosphate dehydrogenase is able to catalyse the conversion of glycerate-1-3-bisphophate to glyceraldehyde-3-phosphate using NADPH or NADH as the cofactor. It displays homology with the family of GAPDH dehydrogenases including both bacterial and human forms, but is unique in its resistance to extremes of temperature.	Defined by 2 residues: CYS:A-140 [auth P-140]HIS:A-219 [auth P-219] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.2.1.12 (PDB Primary Data) Search M-CSA Motif + EC 1.2.1.12 EC: 1.2.1.59 (UniProt) Search M-CSA Motif + EC 1.2.1.59

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.