1L2W | pdb_00001l2w

Crystal Structure of the Yersinia Virulence Effector YopE Chaperone-binding Domain in Complex with its Secretion Chaperone, SycE

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	d1l2wl_	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 YopE domain	(Yersinia pseudotuberculosis ) [TaxId: 633 ],	SCOPe (2.08)
K	d1l2wk_	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 YopE domain	(Yersinia pseudotuberculosis ) [TaxId: 633 ],	SCOPe (2.08)
J	d1l2wj_	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 YopE domain	(Yersinia pseudotuberculosis ) [TaxId: 633 ],	SCOPe (2.08)
I	d1l2wi_	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 YopE domain	(Yersinia pseudotuberculosis ) [TaxId: 633 ],	SCOPe (2.08)
H	d1l2wh_	Alpha and beta proteins (a+b)	Secretion chaperone-like	Type III secretory system chaperone-like	Type III secretory system chaperone	YopE chaperone SycE	(Yersinia pseudotuberculosis ) [TaxId: 633 ],	SCOPe (2.08)
G	d1l2wg_	Alpha and beta proteins (a+b)	Secretion chaperone-like	Type III secretory system chaperone-like	Type III secretory system chaperone	YopE chaperone SycE	(Yersinia pseudotuberculosis ) [TaxId: 633 ],	SCOPe (2.08)
F	d1l2wf_	Alpha and beta proteins (a+b)	Secretion chaperone-like	Type III secretory system chaperone-like	Type III secretory system chaperone	YopE chaperone SycE	(Yersinia pseudotuberculosis ) [TaxId: 633 ],	SCOPe (2.08)
E	d1l2we_	Alpha and beta proteins (a+b)	Secretion chaperone-like	Type III secretory system chaperone-like	Type III secretory system chaperone	YopE chaperone SycE	(Yersinia pseudotuberculosis ) [TaxId: 633 ],	SCOPe (2.08)
D	d1l2wd_	Alpha and beta proteins (a+b)	Secretion chaperone-like	Type III secretory system chaperone-like	Type III secretory system chaperone	YopE chaperone SycE	(Yersinia pseudotuberculosis ) [TaxId: 633 ],	SCOPe (2.08)
C	d1l2wc_	Alpha and beta proteins (a+b)	Secretion chaperone-like	Type III secretory system chaperone-like	Type III secretory system chaperone	YopE chaperone SycE	(Yersinia pseudotuberculosis ) [TaxId: 633 ],	SCOPe (2.08)
B	d1l2wb_	Alpha and beta proteins (a+b)	Secretion chaperone-like	Type III secretory system chaperone-like	Type III secretory system chaperone	YopE chaperone SycE	(Yersinia pseudotuberculosis ) [TaxId: 633 ],	SCOPe (2.08)
A	d1l2wa_	Alpha and beta proteins (a+b)	Secretion chaperone-like	Type III secretory system chaperone-like	Type III secretory system chaperone	YopE chaperone SycE	(Yersinia pseudotuberculosis ) [TaxId: 633 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Type III secretory system chaperone-like	8096292	3000727	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Type III secretory system chaperone-like	8096292	3000727	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Type III secretory system chaperone-like	8096292	3000727	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Type III secretory system chaperone-like	8096292	3000727	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Type III secretory system chaperone-like	8096292	3000727	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Type III secretory system chaperone-like	8096292	3000727	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type III secretory system chaperone-like	8096292	3000727	SCOP2B (2022-06-29)
A	SCOP2 Family	Type III secretory system chaperone	8096291	4003372	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Type III secretory system chaperone-like	8096292	3000727	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	YopE_N	e1l2wL1	A: extended segments	X: Outer membrane virulence protein yopE (From Topology)	H: Outer membrane virulence protein yopE (From Topology)	T: Outer membrane virulence protein yopE	F: YopE_N	ECOD (1.6)
K	YopE_N	e1l2wK1	A: extended segments	X: Outer membrane virulence protein yopE (From Topology)	H: Outer membrane virulence protein yopE (From Topology)	T: Outer membrane virulence protein yopE	F: YopE_N	ECOD (1.6)
J	YopE_N	e1l2wJ1	A: extended segments	X: Outer membrane virulence protein yopE (From Topology)	H: Outer membrane virulence protein yopE (From Topology)	T: Outer membrane virulence protein yopE	F: YopE_N	ECOD (1.6)
I	YopE_N	e1l2wI1	A: extended segments	X: Outer membrane virulence protein yopE (From Topology)	H: Outer membrane virulence protein yopE (From Topology)	T: Outer membrane virulence protein yopE	F: YopE_N	ECOD (1.6)
H	CesT	e1l2wH1	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: CesT	ECOD (1.6)
G	CesT	e1l2wG1	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: CesT	ECOD (1.6)
F	CesT	e1l2wF1	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: CesT	ECOD (1.6)
E	CesT	e1l2wE1	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: CesT	ECOD (1.6)
D	CesT	e1l2wD1	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: CesT	ECOD (1.6)
C	CesT	e1l2wC1	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: CesT	ECOD (1.6)
B	CesT	e1l2wB1	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: CesT	ECOD (1.6)
A	CesT	e1l2wA1	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: CesT	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.30.1460.10	Alpha Beta	2-Layer Sandwich	Yope Regulator	Chain: A,	CATH (4.3.0)
G	3.30.1460.10	Alpha Beta	2-Layer Sandwich	Yope Regulator	Chain: A,	CATH (4.3.0)
F	3.30.1460.10	Alpha Beta	2-Layer Sandwich	Yope Regulator	Chain: A,	CATH (4.3.0)
E	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)
C	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)
A	3.30.1460.10	Alpha Beta	2-Layer Sandwich	Yope Regulator	Chain: A,	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	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I, J, K, L	Outer membrane virulence protein yopE	GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity	regulation of localization import into cell regulation of cellular process regulation of cellular component organization transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis vesicle-mediated transport cellular component organization localization negative regulation of phagocytosis negative regulation of cellular process phagocytosis regulation of localization import into cell regulation of cellular process regulation of cellular component organization transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis vesicle-mediated transport cellular component organization localization negative regulation of phagocytosis negative regulation of cellular process phagocytosis cellular component organization or biogenesis regulation of endocytosis regulation of biological process negative regulation of cellular component organization regulation of transport biological regulation regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization cellular process endocytosis	cell periphery cell outer membrane cellular anatomical structure external encapsulating structure membrane cell envelope outer membrane
A, B, C, D, E A, B, C, D, E, F, G, H	YopE regulator	-	establishment of protein localization nitrogen compound transport transport secretion 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 establishment of protein localization nitrogen compound transport transport secretion 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 macromolecule localization cellular process intracellular protein localization	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I, J, K, L	IPR014773	Virulence factor YopE, GAP domain	Domain
I, J, K, L	IPR015110	YopE, N-terminal domain	Domain
I, J, K, L	IPR003537	Type III secretion system effector protein YopE-like	Family
I, J, K, L	IPR037168	Virulence factor YopE, GAP domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR010261	Tir chaperone protein (CesT) family	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR005416	Type III secretion chaperone SycE	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.