1GVN

Crystal Structure of the Plasmid Maintenance System epsilon/zeta: Meachnism of toxin inactivation and toxin function

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)
B	d1gvnb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Plasmid maintenance system epsilon/zeta, toxin zeta subunit	Plasmid maintenance system epsilon/zeta, toxin zeta subunit	(Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)
D	d1gvnd_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Plasmid maintenance system epsilon/zeta, toxin zeta subunit	Plasmid maintenance system epsilon/zeta, toxin zeta subunit	(Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)
A	d1gvna_	All alpha proteins	immunoglobulin/albumin-binding domain-like	Plasmid maintenance system epsilon/zeta, antidote epsilon subunit	Plasmid maintenance system epsilon/zeta, antidote epsilon subunit	Plasmid maintenance system epsilon/zeta, antidote epsilon subunit	(Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)
C	d1gvnc_	All alpha proteins	immunoglobulin/albumin-binding domain-like	Plasmid maintenance system epsilon/zeta, antidote epsilon subunit	Plasmid maintenance system epsilon/zeta, antidote epsilon subunit	Plasmid maintenance system epsilon/zeta, antidote epsilon subunit	(Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Zeta toxin-like	8019178	4003002	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	P-loop nucleotide/nucleoside kinase-like	8019180	3002021	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8019180	3002021	SCOP2B (2022-06-29)
A	SCOP2 Family	epsilon antitoxin-like	8019188	4002284	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	epsilon antitoxin-like	8019189	3001049	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	epsilon antitoxin-like	8019189	3001049	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)
B	Zeta_toxin	e1gvnB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Zeta_toxin	ECOD (1.6)
D	Zeta_toxin	e1gvnD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Zeta_toxin	ECOD (1.6)
A	Epsilon_antitox	e1gvnA1	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Plasmid maintenance system epsilon/zeta, antidote epsilon subunit (From Topology)	T: Plasmid maintenance system epsilon/zeta, antidote epsilon subunit	F: Epsilon_antitox	ECOD (1.6)
C	Epsilon_antitox	e1gvnC1	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Plasmid maintenance system epsilon/zeta, antidote epsilon subunit (From Topology)	T: Plasmid maintenance system epsilon/zeta, antidote epsilon subunit	F: Epsilon_antitox	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	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)
A	1.10.8.130	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	1.10.8.130	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF06414	Zeta toxin (Zeta_toxin)	Zeta toxin	This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmi ...	This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid [1].	Domain
A, C	PF08998	Bacterial epsilon antitoxin (Epsilon_antitox)	Bacterial epsilon antitoxin	The epsilon antitoxin, produced by various prokaryotes, forms part of a postsegregational killing system which is involved in the initiation of programmed cell death of plasmid-free cells. The protein is folded into a three-helix bundle that directly ...	The epsilon antitoxin, produced by various prokaryotes, forms part of a postsegregational killing system which is involved in the initiation of programmed cell death of plasmid-free cells. The protein is folded into a three-helix bundle that directly interacts with the zeta toxin, inactivating it [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	ZETA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process	-
A, C	EPSILON	binding toxic substance binding	response to stimulus response to chemical response to toxic substance regulation of biological process regulation of cellular process biological regulation negative regulation of cellular process negative regulation of biological process regulation of cell killing cellular process negative regulation of cell killing cell killing	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR010488	Zeta toxin domain	Domain
B, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C	IPR035569	Antitoxin epsilon/PezA domain superfamily	Homologous Superfamily
A, C	IPR015090	Bacterial epsilon antitoxin	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.