3ZVK

Crystal structure of VapBC2 from Rickettsia felis bound to a DNA fragment from their promoter

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PIN	e3zvkA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: PIN	ECOD (1.6)
B	PIN	e3zvkB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: PIN	ECOD (1.6)
C	PIN	e3zvkC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: PIN	ECOD (1.6)
D	PIN	e3zvkD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: PIN	ECOD (1.6)
E	UNK_F_TYPE	e3zvkE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: AbrB	F: UNK_F_TYPE	ECOD (1.6)
F	UNK_F_TYPE	e3zvkF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: AbrB	F: UNK_F_TYPE	ECOD (1.6)
G	UNK_F_TYPE	e3zvkG1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: AbrB	F: UNK_F_TYPE	ECOD (1.6)
H	UNK_F_TYPE	e3zvkH1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: AbrB	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
B	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
C	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
D	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01850	PIN domain (PIN)	PIN domain		Domain
E, F, G, H	PF04014	Antidote-toxin recognition MazE, bacterial antitoxin (MazE_antitoxin)	Antidote-toxin recognition MazE, bacterial antitoxin	AbrB-like is a family of small proteins that operate in conjunction with a cognate toxin molecule. The commonly attributed role of toxin-antitoxin systems is to maintain low-copy number plasmids from one generation to the next. Such gene-pairs are al ...	AbrB-like is a family of small proteins that operate in conjunction with a cognate toxin molecule. The commonly attributed role of toxin-antitoxin systems is to maintain low-copy number plasmids from one generation to the next. Such gene-pairs are also found on chromosomes and to be associated with a number of biological functions such as: reduction of protein synthesis, gene regulation and retardation of cell growth under nutritional stress [1]. This family includes proteins from a number of different pairings, eg MazE, AbrB, VapB [2], PhoU, PemI-like and SpoVT. MazE is the antidote to the toxin MazF of E. coli. MazE-MazF in E. coli is a regulated prokaryotic chromosomal addiction module. MazE antidote is degraded by the ClpPA protease of the bacterial proteasome. MazE-MazF is thought to play a role in programmed cell death when cells suffer nutrient deprivation [3], and MazE-MazF modules have also been implicated in the bacteriostatic effects of other addiction modules [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	TOXIN OF TOXIN-ANTITOXIN SYSTEM	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity	-	-
E, F, G, H	ANTITOXIN OF TOXIN-ANTITOXIN SYSTEM VAPB	DNA binding binding nucleic acid binding	-	-
I [auth X]	DNA	-	-	-
J [auth Y]	DNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002716	PIN domain	Domain
A, B, C, D	IPR029060	PIN-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR022907	VapC family	Family
A, B, C, D	IPR050556	Type II toxin-antitoxin system RNase	Family
E, F, G, H	IPR051734	Type II toxin-antitoxin VapB antitoxins	Family
E, F, G, H	IPR047976	Antitoxin VapB2-like	Family
E, F, G, H	IPR037914	SpoVT-AbrB domain superfamily	Homologous Superfamily
E, F, G, H	IPR007159	SpoVT-AbrB domain	Domain

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.