1NLZ | pdb_00001nlz

Crystal structure of unliganded traffic ATPase of the type IV secretion system of helicobacter pylori

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	d1nlza_	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	d1nlzb_	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	d1nlzc_	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	d1nlzd_	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	d1nlze_	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)
F	d1nlzf_	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)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8018119	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	T2SE N-terminal domain-like	8056589	3002353	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	T2SE N-terminal domain-like	8056589	3002353	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8018119	3002019	SCOP2B (2022-06-29)
C	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)
D	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)
E	SCOP2B Superfamily	RecA-like P-loop NTPases	8018119	3002019	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RecA-like P-loop NTPases	8018119	3002019	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	T2SE N-terminal domain-like	8056589	3002353	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	T2SSE	e1nlzA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: T2SSE	ECOD (1.6)
B	T2SSE	e1nlzB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: T2SSE	ECOD (1.6)
C	T2SSE	e1nlzC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: T2SSE	ECOD (1.6)
D	T2SSE	e1nlzD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: T2SSE	ECOD (1.6)
E	T2SSE	e1nlzE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: T2SSE	ECOD (1.6)
F	T2SSE	e1nlzF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: T2SSE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00437	Type II/IV secretion system protein (T2SSE)	Type II/IV secretion system protein	This entry contains both Type II protein secretion system (T2SS), including Type 4 pilus (T4P), and Type IV protein secretion system (T4SS) from Gram-negative bacteria. Swiss:P07169 VirB11 ATPase is a subunit of the Agrobacterium tumefaciens transfer ...	This entry contains both Type II protein secretion system (T2SS), including Type 4 pilus (T4P), and Type IV protein secretion system (T4SS) from Gram-negative bacteria. Swiss:P07169 VirB11 ATPase is a subunit of the Agrobacterium tumefaciens transfer DNA (T-DNA) transfer system, a type IV secretion pathway required for delivery of T-DNA and effector proteins to plant cells during infection [1]. The cytoplasmic T2S E ATPase is a Zn-containing protein thought to provide the mechanical force for the secretion process. T2S-E contains Walker A and B motifs, that are essential for secretion and ATPase activity. ATPase PulE and XcpR from Klebsiella oxytoca and Pseudomonas aeruginosa respectively are required for protein secretion via the T2SS. ATPase PilB is required for T4P extension [2]. The type II protein secretion system (T2SS) is a sophisticated multi-protein machinery containing 12-15 different proteins [3]. Historically, this system was described as the main terminal branch (MTB) of the general secretory pathway (GSP), but this nomenclature is now on obsolete [4].	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	virB11 homolog	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
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	IPR014155	Type IV secretion system protein VirB11	Family
A, B, C, D, E A, B, C, D, E, F	IPR050921	Type IV secretion system, general secretion pathway E ATPase	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.