1MKI

Crystal Structure of Bacillus Subtilis Probable Glutaminase, APC1040

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
Protein Modification Annotation
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	d1mkia1	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Glutaminase	Probable glutaminase YbgJ	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1mkia2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1mkib1	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Glutaminase	Probable glutaminase YbgJ	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1mkib2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)
A	SCOP2 Family	Glutaminase	8020486	4003774	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	beta-lactamase/transpeptidase-like	8032866	3001604	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8032866	3001604	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	Glutaminase_2nd	e1mkiA1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Glutaminase_2nd	ECOD (1.6)
A	Glutaminase_1st	e1mkiA2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Glutaminase_1st	ECOD (1.6)
B	Glutaminase_2nd	e1mkiB1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Glutaminase_2nd	ECOD (1.6)
B	Glutaminase_1st	e1mkiB2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Glutaminase_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
A	1.10.1500.10	Mainly Alpha	Orthogonal Bundle	Probable Glutaminase Ybgj	Chain: A, domain 2	CATH (4.3.0)
B	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
B	1.10.1500.10	Mainly Alpha	Orthogonal Bundle	Probable Glutaminase Ybgj	Chain: A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF04960	Glutaminase (Glutaminase)	Glutaminase	This family of enzymes deaminates glutamine to glutamate EC:3.5.1.2.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Probable Glutaminase ybgJ	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	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 organic substance metabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process organonitrogen compound catabolic 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 organic substance metabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process organonitrogen compound catabolic process glutamine metabolic process organonitrogen compound metabolic process glutamine catabolic process cellular metabolic 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 metabolic process cellular process small molecule catabolic process organic substance catabolic process glutamine family amino acid biosynthetic process cellular biosynthetic process organonitrogen compound biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process glutamate metabolic process organic substance biosynthetic process dicarboxylic acid biosynthetic process small molecule biosynthetic process dicarboxylic acid metabolic process L-amino acid biosynthetic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process glutamate biosynthetic process alpha-amino acid biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015868	Glutaminase	Family
A, B	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	MSE	Parent Component: MET
A, B	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

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

Chains	Enzyme Name	Description	Catalytic Residues
A	glutaminase M-CSA #301	Glutaminases (EC:3.5.1.2) deaminate glutamine to glutamate. In Bacillus subtilis, glutaminase is encoded by glnA, which is part of an operon, glnA-glnT (formerly ybgJ-ybgH), where glnT encodes a glutamine transporter. The glnA-glnT operon is regulated by the 2-component system GlnK-GlnL in response to glutamine [PMID:15995196].	Defined by 5 residues: SER:A-77 [auth A-74]LYS:A-80 [auth A-77]TYR:A-204 [auth A-201]TYR:A-256 [auth A-253]VAL:A-274 [auth A-271] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.5.1.2 (PDB Primary Data) Search M-CSA Motif + EC 3.5.1.2

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.