2DGM | pdb_00002dgm

Crystal structure of Escherichia coli GadB in complex with iodide

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2dgma_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Pyridoxal-dependent decarboxylase	Glutamate decarboxylase beta, GadB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2dgmb_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Pyridoxal-dependent decarboxylase	Glutamate decarboxylase beta, GadB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2dgmc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Pyridoxal-dependent decarboxylase	Glutamate decarboxylase beta, GadB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2dgmd_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Pyridoxal-dependent decarboxylase	Glutamate decarboxylase beta, GadB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2dgme_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Pyridoxal-dependent decarboxylase	Glutamate decarboxylase beta, GadB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2dgmf_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Pyridoxal-dependent decarboxylase	Glutamate decarboxylase beta, GadB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PLP-dependent transferases	8038947	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8038947	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8038947	3000954	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLP-dependent transferases	8038947	3000954	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PLP-dependent transferases	8038947	3000954	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PLP-dependent transferases	8038947	3000954	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		e2dgmA2	A: alpha bundles	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase	T: Glutamine synthetase/guanido kinase	F:	ECOD (develop294)
B		e2dgmB2	A: alpha bundles	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase	T: Glutamine synthetase/guanido kinase	F:	ECOD (develop294)
C		e2dgmC2	A: alpha bundles	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase	T: Glutamine synthetase/guanido kinase	F:	ECOD (develop294)
D		e2dgmD2	A: alpha bundles	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase	T: Glutamine synthetase/guanido kinase	F:	ECOD (develop294)
E		e2dgmE2	A: alpha bundles	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase	T: Glutamine synthetase/guanido kinase	F:	ECOD (develop294)
F		e2dgmF2	A: alpha bundles	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase	T: Glutamine synthetase/guanido kinase	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	4.10.280.50	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B		CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	3.90.1150.160	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
B	4.10.280.50	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B		CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	3.90.1150.160	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
C	4.10.280.50	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B		CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C	3.90.1150.160	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
D	4.10.280.50	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B		CATH (4.3.0)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
D	3.90.1150.160	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
E	4.10.280.50	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B		CATH (4.3.0)
E	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
E	3.90.1150.160	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
F	4.10.280.50	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B		CATH (4.3.0)
F	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
F	3.90.1150.160	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00282	Pyridoxal-dependent decarboxylase conserved domain (Pyridoxal_deC)	Pyridoxal-dependent decarboxylase conserved domain		Domain

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 decarboxylase beta	glutamate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding	catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process dicarboxylic acid catabolic process alpha-amino acid metabolic process 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 catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process dicarboxylic acid catabolic process alpha-amino acid metabolic process 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 L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process cellular process small molecule catabolic process homeostatic process biological regulation regulation of intracellular pH cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis intracellular chemical homeostasis regulation of biological quality monoatomic cation homeostasis intracellular pH elevation regulation of cellular pH intracellular monoatomic ion homeostasis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR010107	Glutamate decarboxylase	Family
A, B, C, D, E A, B, C, D, E, F	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR002129	Pyridoxal phosphate-dependent decarboxylase, major domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR021115	Pyridoxal-phosphate binding site	Binding Site

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.