5JEN

Crystal structure of the anti-sigma factor RsiV bound to lysozyme

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	d5jenb_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	automated matches	automated matches	(Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
D	d5jend_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	automated matches	automated matches	(Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Peptidoglycan deacetylase N-terminal noncatalytic region	8092030	3000265	SCOP2B (2022-06-29)
C	SCOP2 Family	MPT64-like	8046917	4005367	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Peptidoglycan deacetylase N-terminal noncatalytic region	8092030	3000265	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Lysozyme-like	8037428	3001879	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Lysozyme-like	8037428	3001879	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	DUF3298	e5jenA1	A: a+b two layers	X: Peptidoglycan deacetylase N-terminal noncatalytic region (From Topology)	H: Peptidoglycan deacetylase N-terminal noncatalytic region (From Topology)	T: Peptidoglycan deacetylase N-terminal noncatalytic region	F: DUF3298	ECOD (1.6)
C	DUF3298	e5jenC1	A: a+b two layers	X: Peptidoglycan deacetylase N-terminal noncatalytic region (From Topology)	H: Peptidoglycan deacetylase N-terminal noncatalytic region (From Topology)	T: Peptidoglycan deacetylase N-terminal noncatalytic region	F: DUF3298	ECOD (1.6)
B	Lys	e5jenB1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Lys	ECOD (1.6)
D	Lys	e5jenD1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Lys	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.565.40	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Fervidobacterium nodosum Rt17-B1 like	CATH (4.3.0)
A	3.90.640.20	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
C	3.30.565.40	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Fervidobacterium nodosum Rt17-B1 like	CATH (4.3.0)
C	3.90.640.20	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
B	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
D	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF13739	Deacetylase PdaC (PdaC)	Deacetylase PdaC	This domain forms an alpha-beta-two layer sandwich. It is found in the Bacillus subtilis proteins anti-sigma-V factor RsiV, which downregulates SigV activity [1], and peptidoglycan-N-acetylmuramic acid deacetylase PdaC, which catalyzes the deacetylat ...	This domain forms an alpha-beta-two layer sandwich. It is found in the Bacillus subtilis proteins anti-sigma-V factor RsiV, which downregulates SigV activity [1], and peptidoglycan-N-acetylmuramic acid deacetylase PdaC, which catalyzes the deacetylation of N-acetylmuramic acid which makes the peptidoglycan resistant to lysosyme [2]. It is found in association with Heat-shock cognate 70kd protein 44kd ATPase, Pfam:PF11738.	Domain
A, C	PF11738	Protein of unknown function (DUF3298) (DUF3298)	Protein of unknown function (DUF3298)	This family of bacterial protein C-terminal regions is highly conserved but the function is not known. Several members are annotated as being endo-1,4-beta-xylanase-like, but this could not be confirmed, and the structure can be defined as a heat-sho ...	This family of bacterial protein C-terminal regions is highly conserved but the function is not known. Several members are annotated as being endo-1,4-beta-xylanase-like, but this could not be confirmed, and the structure can be defined as a heat-shock cognate 70kd protein 44kd ATPase.	Domain
B, D	PF00062	C-type lysozyme/alpha-lactalbumin family (Lys)	C-type lysozyme/alpha-lactalbumin family	Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bac ...	Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bacterial cell walls. Structure is a multi-domain, mixed alpha and beta fold, containing four conserved disulfide bonds.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Anti-sigma-V factor RsiV	-	-	cell periphery plasma membrane membrane cellular anatomical entity
B, D	Lysozyme C	hydrolase activity, acting on glycosyl bonds hexosaminidase activity beta-N-acetylhexosaminidase activity beta-N-acetylglucosaminidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity peptidoglycan muralytic activity lysozyme activity identical protein binding protein binding binding	organic substance metabolic process catabolic process cell wall organization or biogenesis metabolic process cellular process macromolecule metabolic process organic substance catabolic process macromolecule catabolic process cell wall macromolecule catabolic process cell wall macromolecule metabolic process biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism organic substance metabolic process catabolic process cell wall organization or biogenesis metabolic process cellular process macromolecule metabolic process organic substance catabolic process macromolecule catabolic process cell wall macromolecule catabolic process cell wall macromolecule metabolic process biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing response to stimulus response to other organism defense response response to external stimulus defense response to Gram-negative bacterium response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus defense response to Gram-positive bacterium	intracellular anatomical structure cytoplasm cellular anatomical entity extracellular region extracellular space membrane-bounded organelle intracellular organelle organelle endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR037126	PdaC/RsiV-like superfamily	Homologous Superfamily
A, C	IPR021729	Domain of unknown function DUF3298	Domain
A, C	IPR025303	Deacetylase PdaC	Domain
B, D	IPR001916	Glycoside hydrolase, family 22	Family
B, D	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
B, D	IPR019799	Glycoside hydrolase family 22 domain	Domain
B, D	IPR000974	Glycoside hydrolase, family 22, lysozyme	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.