4MCX

P. vulgaris HIGBA structure, crystal form 2

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4mcxa_	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	SinR domain-like	Antitoxin HigA	(Proteus vulgaris ) [TaxId: 585 ],	SCOPe (2.08)
C	d4mcxc_	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	SinR domain-like	Antitoxin HigA	(Proteus vulgaris ) [TaxId: 585 ],	SCOPe (2.08)
E	d4mcxe_	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	SinR domain-like	Antitoxin HigA	(Proteus vulgaris ) [TaxId: 585 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	RelE-like	8102970	3000741	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RelE-like	8102970	3000741	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RelE-like	8102970	3000741	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8082923	3000119	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8082923	3000119	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8082923	3000119	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	HigB-like_toxin	e4mcxB1	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	e4mcxD1	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	e4mcxF1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: HigB-like_toxin	ECOD (1.6)
A	HTH_3_3	e4mcxA1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: HTH_3_3	ECOD (1.6)
C	HTH_3_3	e4mcxC1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: HTH_3_3	ECOD (1.6)
E	HTH_3_3	e4mcxE1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: HTH_3_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	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)
F	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
A	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
C	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
E	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F	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
A, C, E	PF01381	Helix-turn-helix (HTH_3)	Helix-turn-helix	This large family of DNA binding helix-turn helix proteins includes Cro Swiss:P03036 and CI Swiss:P03034. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be ...	This large family of DNA binding helix-turn helix proteins includes Cro Swiss:P03036 and CI Swiss:P03034. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteristic of the whole family [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F	Killer protein	endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity RNA binding binding organic cyclic compound 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 organic cyclic compound catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process organic substance catabolic process catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process organic substance catabolic process RNA catabolic process cellular 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 cellular biosynthetic process organonitrogen compound biosynthetic process negative regulation of cellular metabolic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation organic substance biosynthetic process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular 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	-
A, C, E	Antidote protein	protein heterodimerization activity protein binding binding protein dimerization activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity protein heterodimerization activity protein binding binding protein dimerization activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity molecular sequestering activity toxin sequestering activity	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F	IPR007711	Toxin HigB-1	Family
B, D, F	IPR035093	Toxin-antitoxin system, RelE/ParE toxin domain superfamily	Homologous Superfamily
A, C, E	IPR001387	Cro/C1-type helix-turn-helix domain	Domain
A, C, E	IPR013430	Toxin-antitoxin system, antidote protein, HigA	Family
A, C, E	IPR010982	Lambda repressor-like, DNA-binding domain superfamily	Homologous Superfamily

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.