2YFH | pdb_00002yfh

Structure of a Chimeric Glutamate Dehydrogenase

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2yfha2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	([Clostridium] symbiosum ) [TaxId: 1512 ], (Escherichia coli ) [TaxId: 562 ], ([Clostridium] symbiosum ) [TaxId: 1512 ],	SCOPe (2.08)
A	d2yfha1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenases	automated matches	([Clostridium] symbiosum ) [TaxId: 1512 ], (Escherichia coli ) [TaxId: 562 ], ([Clostridium] symbiosum ) [TaxId: 1512 ],	SCOPe (2.08)
B	d2yfhb2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	([Clostridium] symbiosum ) [TaxId: 1512 ], (Escherichia coli ) [TaxId: 562 ], ([Clostridium] symbiosum ) [TaxId: 1512 ],	SCOPe (2.08)
B	d2yfhb1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenases	automated matches	([Clostridium] symbiosum ) [TaxId: 1512 ], (Escherichia coli ) [TaxId: 562 ], ([Clostridium] symbiosum ) [TaxId: 1512 ],	SCOPe (2.08)
C	d2yfhc2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	([Clostridium] symbiosum ) [TaxId: 1512 ], (Escherichia coli ) [TaxId: 562 ], ([Clostridium] symbiosum ) [TaxId: 1512 ],	SCOPe (2.08)
C	d2yfhc1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenases	automated matches	([Clostridium] symbiosum ) [TaxId: 1512 ], (Escherichia coli ) [TaxId: 562 ], ([Clostridium] symbiosum ) [TaxId: 1512 ],	SCOPe (2.08)
D	d2yfhd2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	([Clostridium] symbiosum ) [TaxId: 1512 ], (Escherichia coli ) [TaxId: 562 ], ([Clostridium] symbiosum ) [TaxId: 1512 ],	SCOPe (2.08)
D	d2yfhd1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenases	automated matches	([Clostridium] symbiosum ) [TaxId: 1512 ], (Escherichia coli ) [TaxId: 562 ], ([Clostridium] symbiosum ) [TaxId: 1512 ],	SCOPe (2.08)
E	d2yfhe2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	([Clostridium] symbiosum ) [TaxId: 1512 ], (Escherichia coli ) [TaxId: 562 ], ([Clostridium] symbiosum ) [TaxId: 1512 ],	SCOPe (2.08)
E	d2yfhe1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenases	automated matches	([Clostridium] symbiosum ) [TaxId: 1512 ], (Escherichia coli ) [TaxId: 562 ], ([Clostridium] symbiosum ) [TaxId: 1512 ],	SCOPe (2.08)
F	d2yfhf2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	([Clostridium] symbiosum ) [TaxId: 1512 ], (Escherichia coli ) [TaxId: 562 ], ([Clostridium] symbiosum ) [TaxId: 1512 ],	SCOPe (2.08)
F	d2yfhf1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenases	automated matches	([Clostridium] symbiosum ) [TaxId: 1512 ], (Escherichia coli ) [TaxId: 562 ], ([Clostridium] symbiosum ) [TaxId: 1512 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	MtdA-like	8056050	3000046	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MtdA-like	8056050	3000046	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MtdA-like	8056050	3000046	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MtdA-like	8056050	3000046	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	MtdA-like	8056050	3000046	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	MtdA-like	8056050	3000046	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		e2yfhA1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: NTP_transf_2	F:	ECOD (20:10:01)
A		e2yfhA2	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: Ldh_1_C	F:	ECOD (20:10:01)
B		e2yfhB1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: ABC_tran	F:	ECOD (20:10:01)
B		e2yfhB2	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: Ldh_1_C	F:	ECOD (20:10:01)
C		e2yfhC1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: ABC_tran	F:	ECOD (20:10:01)
C		e2yfhC2	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: Ldh_1_C	F:	ECOD (20:10:01)
D		e2yfhD1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: ABC_tran	F:	ECOD (20:10:01)
D		e2yfhD2	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: Ldh_1_C	F:	ECOD (20:10:01)
E		e2yfhE1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: ABC_tran	F:	ECOD (20:10:01)
E		e2yfhE2	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: Ldh_1_C	F:	ECOD (20:10:01)
F		e2yfhF1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: ABC_tran	F:	ECOD (20:10:01)
F		e2yfhF2	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: Ldh_1_C	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	CATH (4.3.0)
A	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	CATH (4.3.0)
B	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	CATH (4.3.0)
C	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	CATH (4.3.0)
D	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	CATH (4.3.0)
E	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F	1.10.285.10	Mainly Alpha	Orthogonal Bundle	Glutamate Dehydrogenase	Chain A, domain 3	CATH (4.3.0)
F	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE	oxidoreductase activity, acting on the CH-NH2 group of donors amino-acid dehydrogenase [NAD(P)+] activity oxidoreductase activity L-glutamate dehydrogenase [NAD(P)+] activity L-glutamate dehydrogenase (NAD+) activity oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor catalytic activity L-glutamate dehydrogenase (NADP+) activity	L-glutamate fermentation via 2-hydroxyglutarate catabolic process oxoacid metabolic process energy derivation by oxidation of organic compounds amino acid metabolic process organic acid catabolic process organic acid metabolic process dicarboxylic acid catabolic process alpha-amino acid metabolic process fermentation carboxylic acid catabolic process glutamate metabolic process small molecule metabolic process amino acid catabolic process L-glutamate fermentation via 2-hydroxyglutarate catabolic process oxoacid metabolic process energy derivation by oxidation of organic compounds amino acid metabolic process organic acid catabolic process organic acid metabolic process dicarboxylic acid catabolic process alpha-amino acid metabolic process fermentation carboxylic acid catabolic process glutamate metabolic process small molecule metabolic process amino acid catabolic process L-glutamate catabolic process dicarboxylic acid metabolic process L-amino acid catabolic process carboxylic acid metabolic process primary metabolic process generation of precursor metabolites and energy L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process amino acid fermentation metabolic process cellular process small molecule catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR006095	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F	IPR046346	Aminoacid dehydrogenase-like, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006096	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050724	Glutamate/Leucine/Phenylalanine/Valine dehydrogenases	Family
A, B, C, D, E A, B, C, D, E, F	IPR006097	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, dimerisation domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014362	Glutamate dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F	IPR033524	Leu/Phe/Val dehydrogenases active site	Active Site
A, B, C, D, E A, B, C, D, E, F	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR033922	NAD(P) binding domain of glutamate dehydrogenase	Domain

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.