5IXL | pdb_00005ixl

Structure of P. vulgaris HigB toxin Y91A variant

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	RelE-like	8102970	3000741	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RelE-like	8102970	3000741	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RelE-like	8102970	3000741	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RelE-like	8102970	3000741	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RelE-like	8102970	3000741	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RelE-like	8102970	3000741	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RelE-like	8102970	3000741	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RelE-like	8102970	3000741	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	HigB-like_toxin	e5ixlH1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: HigB-like_toxin	ECOD (1.6)
G	HigB-like_toxin	e5ixlG1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: HigB-like_toxin	ECOD (1.6)
F	HigB-like_toxin	e5ixlF1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: HigB-like_toxin	ECOD (1.6)
E	HigB-like_toxin	e5ixlE1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: HigB-like_toxin	ECOD (1.6)
D	HigB-like_toxin	e5ixlD1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: HigB-like_toxin	ECOD (1.6)
C	HigB-like_toxin	e5ixlC1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: HigB-like_toxin	ECOD (1.6)
B	HigB-like_toxin	e5ixlB1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: HigB-like_toxin	ECOD (1.6)
A	HigB-like_toxin	e5ixlA1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: HigB-like_toxin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
G	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
F	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
E	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
D	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
C	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
B	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
A	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	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	PF05015	RelE-like toxin of type II toxin-antitoxin system HigB (HigB-like_toxin)	RelE-like toxin of type II toxin-antitoxin system HigB	This family carries several different examples of type II bacterial toxins of toxin-antitoxin systems including many HigB-like ones. The fold is referred to as the RelE/YoeB/Txe/Yeeu fold suggesting all examples of these are present in this family. S ...	This family carries several different examples of type II bacterial toxins of toxin-antitoxin systems including many HigB-like ones. The fold is referred to as the RelE/YoeB/Txe/Yeeu fold suggesting all examples of these are present in this family. Several plasmids with proteic killer gene-systems have been reported. All of them encode a stable toxin and an unstable antidote. Upon loss of the plasmid, the less stable inhibitor is inactivated more rapidly than the toxin, allowing the toxin to be activated. The activation of these systems results in cell filamentation and cessation of viable cell production. It has been verified that both the stable killer and the unstable inhibitor of the systems are short polypeptides. This family corresponds to the toxin [1,2].	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, G, H	Endoribonuclease HigB	endonuclease activity nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity RNA binding binding nucleic acid binding mRNA binding translation regulator activity translation repressor activity ribonucleoprotein complex binding endonuclease activity nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity RNA binding binding nucleic acid binding mRNA binding translation regulator activity translation repressor activity ribonucleoprotein complex binding protein-containing complex binding ribosome binding	catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process plasmid maintenance regulation of biological process catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process plasmid maintenance regulation of biological process regulation of growth regulation of cellular component organization regulation of cellular process negative regulation of biological process biological regulation growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth negative regulation of cellular process cellular component organization or biogenesis protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of protein metabolic process negative regulation of metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR007711	Toxin HigB-1	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR035093	Toxin-antitoxin system, RelE/ParE toxin domain superfamily	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.