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)
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)
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	MtdA-like	8056050	3000046	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	MtdA-like	8056050	3000046	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MtdA-like	8056050	3000046	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MtdA-like	8056050	3000046	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MtdA-like	8056050	3000046	SCOP2B (2022-06-29)
A	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)
F	ABC_tran	e2yfhF1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (v294.1)
F	EPSP_synthase	e2yfhF2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)
E	ABC_tran	e2yfhE1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (v294.1)
E	EPSP_synthase	e2yfhE2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)
D	ABC_tran	e2yfhD1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (v294.1)
D	EPSP_synthase	e2yfhD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)
C	ABC_tran	e2yfhC1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (v294.1)
C	EPSP_synthase	e2yfhC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)
B	ABC_tran	e2yfhB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (v294.1)
B	EPSP_synthase	e2yfhB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)
A	NTP_transf_2	e2yfhA1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: NTP_transf_2	ECOD (v294.1)
A	EPSP_synthase	e2yfhA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)
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)
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)

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	amino acid metabolic process primary metabolic process metabolic process cellular 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.