2PT7 | pdb_00002pt7

Crystal structure of Cag VirB11 (HP0525) and an inhibitory protein (HP1451)

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)
F	d2pt7f_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Hexameric traffic ATPase, HP0525	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
E	d2pt7e_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Hexameric traffic ATPase, HP0525	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
D	d2pt7d_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Hexameric traffic ATPase, HP0525	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
C	d2pt7c_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Hexameric traffic ATPase, HP0525	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
B	d2pt7b_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Hexameric traffic ATPase, HP0525	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
A	d2pt7a_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Hexameric traffic ATPase, HP0525	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	T2SE N-terminal domain-like	8056589	3002353	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RecA-like P-loop NTPases	8018119	3002019	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RecA-like P-loop NTPases	8018119	3002019	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	T2SE N-terminal domain-like	8056589	3002353	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8018119	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	T2SE N-terminal domain-like	8056589	3002353	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	T2SE N-terminal domain-like	8056589	3002353	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8018119	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8018119	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	T2SE N-terminal domain-like	8056589	3002353	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	T2SE N-terminal domain-like	8056589	3002353	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8018119	3002019	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)
H	Lipase_3	e2pt7H5	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Lipase_3	ECOD (develop294)
G		e2pt7G5	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F:	ECOD (develop294)
G	Prenyltrans	e2pt7G6	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Prenyltrans	ECOD (develop294)
F	Pyr_redox_2	e2pt7F1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (develop294)
E	Pyr_redox_2	e2pt7E1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (develop294)
D	Helicase_C	e2pt7D1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Helicase_C	ECOD (develop294)
C	Pyr_redox_2	e2pt7C1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (develop294)
B	Pyr_redox_2	e2pt7B1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (develop294)
A	Helicase_C	e2pt7A1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Helicase_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.30.300.20	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
H	3.30.1370.180	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
G	3.30.300.20	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
G	3.30.1370.180	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
F	3.30.450.90	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	3.30.450.90	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.30.450.90	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.30.450.90	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.30.450.90	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.30.450.90	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G, H	PF18472	HP1451 C-terminal domain (HP1451_C)	HP1451 C-terminal domain	HP1451 modulates the ATPase activity of HP0525 H. pylori. It is suggested that HP1451 acts as an inhibitory factor of HP0525 to regulate Cag-mediated secretion. It consists of two domains. The two HP1451 domains (referred to as the KH-domain and S8-d ...	HP1451 modulates the ATPase activity of HP0525 H. pylori. It is suggested that HP1451 acts as an inhibitory factor of HP0525 to regulate Cag-mediated secretion. It consists of two domains. The two HP1451 domains (referred to as the KH-domain and S8-domain) interact with each other via two salt bridges. The second domain is structurally homologous to other nucleic acid-binding proteins such as the NTD of ribosomal protein S8 and DNaseI [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H	Hypothetical protein	RNA binding binding nucleic acid binding	-	-
A, B, C, D, E A, B, C, D, E, F	Cag-alfa	pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding identical protein binding protein binding	localization secretion by cell secretion transport export from cell secretion by the type IV secretion system cellular process establishment of localization	protein-containing complex type IV secretion system complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G, H	IPR015946	K homology domain-like, alpha/beta	Homologous Superfamily
G, H	IPR038008	Jag, KH domain	Domain
G, H	IPR040977	HP1451, C-terminal	Domain
G, H	IPR038247	Jag, N-terminal domain superfamily	Homologous Superfamily
G, H	IPR039247	RNA-binding protein KhpB	Family
G, H	IPR032782	RNA-binding protein KhpB, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001482	Type II/IV secretion system domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050921	T4SS_GSP_E_ATPase	Unknown
A, B, C, D, E A, B, C, D, E, F	IPR014155	Type IV secretion system protein VirB11	Family
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.