2Z3A

Crystal Structure of Bacillus Subtilis CodW, a non-canonical HslV-like peptidase with an impaired catalytic apparatus

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	d2z3aa_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d2z3ab_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d2z3ac_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d2z3ad_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d2z3ae_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d2z3af_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
H	d2z3ah_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
I	d2z3ai_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
J	d2z3aj_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
K	d2z3ak_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
L	d2z3al_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
G	d2z3ag_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(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	SCOP2B Superfamily	Class II glutamine amidotransferases	8038098	3000131	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II glutamine amidotransferases	8038098	3000131	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class II glutamine amidotransferases	8038098	3000131	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Class II glutamine amidotransferases	8038098	3000131	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Class II glutamine amidotransferases	8038098	3000131	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Class II glutamine amidotransferases	8038098	3000131	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Class II glutamine amidotransferases	8038098	3000131	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Class II glutamine amidotransferases	8038098	3000131	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Class II glutamine amidotransferases	8038098	3000131	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Class II glutamine amidotransferases	8038098	3000131	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Class II glutamine amidotransferases	8038098	3000131	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Class II glutamine amidotransferases	8038098	3000131	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	Proteasome	e2z3aA1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)
B	Proteasome	e2z3aB1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)
C	Proteasome	e2z3aC1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)
D	Proteasome	e2z3aD1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)
E	Proteasome	e2z3aE1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)
F	Proteasome	e2z3aF1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)
H	Proteasome	e2z3aH1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)
I	Proteasome	e2z3aI1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)
J	Proteasome	e2z3aJ1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)
K	Proteasome	e2z3aK1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)
L	Proteasome	e2z3aL1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)
G	Proteasome	e2z3aG1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
B	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
C	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
D	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
E	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
F	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
H	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
I	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
J	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
K	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
L	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
G	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	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, G, H, I, J, K, L	PF00227	Proteasome subunit (Proteasome)	Proteasome subunit	The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologues vary greatly in complexity ...	The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologues vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is encoded by more than 14 genes [1]. Recently evidence of two novel groups of bacterial proteasomes was proposed. The first is Anbu, which is sparsely distributed among cyanobacteria and proteobacteria [1]. The second is call beta-proteobacteria proteasome homologue (BPH) [1].	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, G, H, I, J, K, L	ATP-dependent protease hslV	peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity catalytic activity threonine-type peptidase activity endopeptidase activity threonine-type endopeptidase activity cation binding ion binding binding metal ion binding small molecule binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process	protein-containing complex intracellular anatomical structure catalytic complex peptidase complex cellular anatomical entity cytosolic proteasome complex HslUV protease complex proteasome complex endopeptidase complex cytoplasm cytosol intracellular protein-containing complex proteasome core complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR023333	Proteasome B-type subunit	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR029055	Nucleophile aminohydrolases, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR001353	Proteasome, subunit alpha/beta	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR022281	ATP-dependent protease, HslV subunit	Family

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.