2Z3B | pdb_00002z3b

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)
L	d2z3bl_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
K	d2z3bk_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
J	d2z3bj_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
I	d2z3bi_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
H	d2z3bh_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
G	d2z3bg_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d2z3bf_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d2z3be_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d2z3bd_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d2z3bc_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d2z3bb_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d2z3ba_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(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)
L	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)
J	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)
H	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)
F	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)
D	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)
B	SCOP2B Superfamily	Class II glutamine amidotransferases	8038098	3000131	SCOP2B (2022-06-29)
A	SCOP2 Family	Proteasome subunits	8025719	4002254	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Class II glutamine amidotransferases	8038098	3000131	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)
L		e2z3bL1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
K		e2z3bK1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
J		e2z3bJ1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
I		e2z3bI1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
H		e2z3bH1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
G		e2z3bG1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
F		e2z3bF1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
E		e2z3bE1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
D		e2z3bD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
C		e2z3bC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
B		e2z3bB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
A		e2z3bA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

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

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	-	cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex catalytic complex peptidase complex cytosolic proteasome complex HslUV protease complex proteasome complex endopeptidase complex 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 subunit HslV	Family

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.