3G5O

The crystal structure of the toxin-antitoxin complex RelBE2 (Rv2865-2866) from Mycobacterium tuberculosis

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)
A	SCOP2 Family	YefM-like	8082986	4003460	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YefM-like	8082987	3000907	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	YefM-like	8082987	3000907	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	PhdYeFM_antitox	e3g5oA1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PhdYeFM_antitox	ECOD (1.6)
D	PhdYeFM_antitox	e3g5oD1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PhdYeFM_antitox	ECOD (1.6)
B	ParE_toxin_1	e3g5oB1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: ParE_toxin_1	ECOD (1.6)
C	ParE_toxin_1	e3g5oC1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: ParE_toxin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
A	1.10.1220.170	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant		CATH (4.3.0)
D	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
D	1.10.1220.170	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant		CATH (4.3.0)
B	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF02604	Antitoxin Phd_YefM, type II toxin-antitoxin system (PhdYeFM_antitox)	Antitoxin Phd_YefM, type II toxin-antitoxin system	Members of this family act as antitoxins in type II toxin-antitoxin systems [1]. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin [2] ...	Members of this family act as antitoxins in type II toxin-antitoxin systems [1]. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin [2]. This domain complexes with Txe toxins containing Pfam:PF06769, Fic/DOC toxins containing Pfam:PF02661 and YafO toxins containing Pfam:PF13957.	Domain
B, C	PF05016	ParE toxin of type II toxin-antitoxin system, parDE (ParE_toxin)	ParE toxin of type II toxin-antitoxin system, parDE	ParE is the toxin family of a type II toxin-antitoxin family. It is toxic towards DNA gyrase, but is neutralised by the antitoxin ParD. The family also encompasses RelE/ParE described in [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	Uncharacterized protein Rv2865	DNA binding binding organic cyclic compound binding nucleic acid binding 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 positive regulation of growth regulation of growth positive regulation of biological process growth	-
B, C	Uncharacterized protein Rv2866	DNA binding binding organic cyclic compound binding nucleic acid binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process catabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process organic substance catabolic process RNA catabolic process regulation of growth negative regulation of growth growth	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR006442	Type II toxin-antitoxin system, antitoxin Phd/YefM	Family
A, D	IPR036165	YefM-like superfamily	Homologous Superfamily
B, C	IPR007712	Toxin-antitoxin system, RelE/ParE toxin family	Family
B, C	IPR035093	Toxin-antitoxin system, RelE/ParE toxin 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.