1JYO

Structure of the Salmonella Virulence Effector SptP in Complex with its Secretion Chaperone SicP

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	d1jyoa_	Alpha and beta proteins (a+b)	Secretion chaperone-like	Type III secretory system chaperone-like	Type III secretory system chaperone	Virulence effector SptP secretion chaperone SicP	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
B	d1jyob_	Alpha and beta proteins (a+b)	Secretion chaperone-like	Type III secretory system chaperone-like	Type III secretory system chaperone	Virulence effector SptP secretion chaperone SicP	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
C	d1jyoc_	Alpha and beta proteins (a+b)	Secretion chaperone-like	Type III secretory system chaperone-like	Type III secretory system chaperone	Virulence effector SptP secretion chaperone SicP	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
D	d1jyod_	Alpha and beta proteins (a+b)	Secretion chaperone-like	Type III secretory system chaperone-like	Type III secretory system chaperone	Virulence effector SptP secretion chaperone SicP	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
E	d1jyoe_	Alpha and beta proteins (a+b)	Non-globular alpha+beta subunits of globular proteins	Non-globular alpha+beta subunits of globular proteins	Type III secretory system effector	Virulence effector SptP domain	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
F	d1jyof_	Alpha and beta proteins (a+b)	Non-globular alpha+beta subunits of globular proteins	Non-globular alpha+beta subunits of globular proteins	Type III secretory system effector	Virulence effector SptP domain	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Type III secretory system chaperone	8025098	4003372	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Type III secretory system chaperone-like	8037477	3000727	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Type III secretory system chaperone-like	8037477	3000727	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Type III secretory system chaperone-like	8037477	3000727	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Type III secretory system chaperone-like	8037477	3000727	SCOP2B (2022-06-29)
E	SCOP2 Family	Virulence effector SptP domain	8025100	4003571	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Non-globular alpha+beta subunits of globular proteins	8037479	3001542	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	Non-globular alpha+beta subunits of globular proteins	8037479	3001542	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	PF05932	e1jyoA1	A: a+b two layers	X: Type III secretory system chaperone-like	H: Type III secretory system chaperone (From Topology)	T: Type III secretory system chaperone	F: PF05932	ECOD (1.6)
B	PF05932	e1jyoB1	A: a+b two layers	X: Type III secretory system chaperone-like	H: Type III secretory system chaperone (From Topology)	T: Type III secretory system chaperone	F: PF05932	ECOD (1.6)
C	PF05932	e1jyoC1	A: a+b two layers	X: Type III secretory system chaperone-like	H: Type III secretory system chaperone (From Topology)	T: Type III secretory system chaperone	F: PF05932	ECOD (1.6)
D	PF05932	e1jyoD1	A: a+b two layers	X: Type III secretory system chaperone-like	H: Type III secretory system chaperone (From Topology)	T: Type III secretory system chaperone	F: PF05932	ECOD (1.6)
E	PF09119	e1jyoE1	A: extended segments	X: Virulence effector SptP domain (From Topology)	H: Virulence effector SptP domain (From Topology)	T: Virulence effector SptP domain	F: PF09119	ECOD (1.6)
F	PF09119	e1jyoF1	A: extended segments	X: Virulence effector SptP domain (From Topology)	H: Virulence effector SptP domain (From Topology)	T: Virulence effector SptP domain	F: PF09119	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1460.10	Alpha Beta	2-Layer Sandwich	Yope Regulator	Chain: A,	CATH (4.3.0)
B	3.30.1460.10	Alpha Beta	2-Layer Sandwich	Yope Regulator	Chain: A,	CATH (4.3.0)
C	3.30.1460.10	Alpha Beta	2-Layer Sandwich	Yope Regulator	Chain: A,	CATH (4.3.0)
D	3.30.1460.10	Alpha Beta	2-Layer Sandwich	Yope Regulator	Chain: A,	CATH (4.3.0)
E	4.10.1330.10	Few Secondary Structures	Irregular	non globular Virulence effector SptP fold	non globular Virulence effector SptP domain	CATH (4.3.0)
F	4.10.1330.10	Few Secondary Structures	Irregular	non globular Virulence effector SptP fold	non globular Virulence effector SptP domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF05932	Tir chaperone protein (CesT) family (CesT)	Tir chaperone protein (CesT) family	This family consists of a number of bacterial sequences which are highly similar to the Tir chaperone protein in E. Coli. In many Gram-negative bacteria, a key indicator of pathogenic potential is the possession of a specialised type III secretion sy ...	This family consists of a number of bacterial sequences which are highly similar to the Tir chaperone protein in E. Coli. In many Gram-negative bacteria, a key indicator of pathogenic potential is the possession of a specialised type III secretion system, which is utilised to deliver virulence effector proteins directly into the host cell cytosol. Many of the proteins secreted from such systems require small cytosolic chaperones to maintain the secreted substrates in a secretion-competent state. CesT serves a chaperone function for the enteropathogenic Escherichia coli (EPEC) translocated intimin receptor (Tir) protein, which confers upon EPEC the ability to alter host cell morphology following intimate bacterial attachment [1]. This family also contains several DspF and related sequences from several plant pathogenic bacteria. The "disease-specific" (dsp) region next to the hrp gene cluster of Erwinia amylovora is required for pathogenicity but not for elicitation of the hypersensitive reaction. DspF and AvrF are small (16 kDa and 14 kDa) and acidic with predicted amphipathic alpha helices in their C termini; they resemble chaperones for virulence factors secreted by type III secretion systems of animal pathogens [2].	Domain
E, F	PF09119	SicP binding (SicP-binding)	SicP binding	Members of this family bind the chaperone SicP, which is required both to maintain the stability of SptP, as well as to ensure the eventual secretion of the protein. The domain is found in the Salmonella effector protein SptP, which interacts with Si ...	Members of this family bind the chaperone SicP, which is required both to maintain the stability of SptP, as well as to ensure the eventual secretion of the protein. The domain is found in the Salmonella effector protein SptP, which interacts with SicP chaperone dimers mainly through four regions of its chaperone-binding domain. The structure of the SptP-SicP complex contains four molecules of SicP, aligned in a linear fashion and arranged in two sets of tightly bound homodimers that bind two SptP molecules. The SicP homodimers do not interact with each other, but are held together by a molecular interface formed between two SptP molecules. Each SptP molecule is wrapped around by three SicP chaperones (two chaperones from one homodimer and a third one from the opposite homodimer pair) [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	SicP	-	protein localization establishment of protein localization cellular localization nitrogen compound transport transport secretion organic substance transport protein secretion by the type III secretion system establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization protein localization establishment of protein localization cellular localization nitrogen compound transport transport secretion organic substance transport protein secretion by the type III secretion system establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization secretion by cell protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization cellular process	intracellular anatomical structure cytoplasm cellular anatomical entity
E, F	protein tyrosine phosphatase SptP	GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds protein tyrosine phosphatase activity phosphatase activity hydrolase activity GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds protein tyrosine phosphatase activity phosphatase activity hydrolase activity catalytic activity	dephosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process	extracellular region extracellular space cellular anatomical entity host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR010261	Tir chaperone protein (CesT) family	Family
A, B, C, D	IPR044530	Chaperone protein SicP	Family
E, F	IPR003546	Type III secreted modular tyrosine phosphatase, SptP/YopH	Family
E, F	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
E, F	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
E, F	IPR000242	Tyrosine-specific protein phosphatase, PTPase domain	Domain
E, F	IPR011070	Globular protein, non-globular alpha/beta subunit	Homologous Superfamily
E, F	IPR014773	Virulence factor YopE, GAP domain	Domain
E, F	IPR000387	Tyrosine-specific protein phosphatases domain	Domain
E, F	IPR015203	Secreted effector protein SptP, N-terminal domain	Domain
E, F	IPR016130	Protein-tyrosine phosphatase, active site	Active Site
E, F	IPR044899	Secreted effector protein SptP, N-terminal domain superfamily	Homologous Superfamily
E, F	IPR037168	Virulence factor YopE, GAP domain superfamily	Homologous Superfamily

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 R01GM133198.