2NV0

Structure of the glutaminase subunit Pdx2 (YaaE) of PLP synthase from Bacillus subtilis

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)
B	d2nv0b_	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Class I glutamine amidotransferases (GAT)	Hypothetical protein YaaE	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d2nv0a_	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Class I glutamine amidotransferases (GAT)	Hypothetical protein YaaE	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8043266	3001405	SCOP2B (2022-06-29)
A	SCOP2 Family	Class I glutamine amidotransferases (GAT)	8030887	4003747	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Class I glutamine amidotransferase-like	8043266	3001405	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	GATase	e2nv0B1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
A	GATase	e2nv0A1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
A	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00117	Glutamine amidotransferase class-I (GATase)	Glutamine amidotransferase class-I	-	Domain
A, B	PF01174	SNO glutamine amidotransferase family (SNO)	SNO glutamine amidotransferase family	This family and its amidotransferase domain was first described in [1]. It is predicted that members of this family are involved in the pyridoxine biosynthetic pathway, based on the proximity and co-regulation of the corresponding genes and physical ...	This family and its amidotransferase domain was first described in [1]. It is predicted that members of this family are involved in the pyridoxine biosynthetic pathway, based on the proximity and co-regulation of the corresponding genes and physical interaction between the members of Pfam:PF01174 and Pfam:PF01680 [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Glutamine amidotransferase subunit pdxT	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides glutaminase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds identical protein binding protein binding binding amine-lyase activity lyase activity pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity carbon-nitrogen lyase activity	organic hydroxy compound metabolic process vitamin biosynthetic process aldehyde biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process water-soluble vitamin metabolic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process aldehyde metabolic process organic hydroxy compound metabolic process vitamin biosynthetic process aldehyde biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process water-soluble vitamin metabolic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic hydroxy compound biosynthetic process metabolic process cellular process vitamin B6 metabolic process pyridoxal phosphate metabolic process pyridoxine metabolic process catabolic process oxoacid metabolic process glutamine family amino acid catabolic process amino acid metabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process cellular catabolic process carboxylic acid catabolic process amino acid catabolic process glutamine metabolic process glutamine catabolic process carboxylic acid metabolic process L-amino acid catabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process small molecule catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex glutaminase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029062	Class I glutamine amidotransferase-like	Homologous Superfamily
A, B	IPR002161	Pyridoxal 5'-phosphate synthase subunit PdxT/SNO	Family
A, B	IPR021196	PdxT/SNO family, conserved site	Conserved 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.