4FXE | pdb_00004fxe

Crystal structure of the intact E. coli RelBE toxin-antitoxin complex

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)
B	SCOP2B Superfamily	Ribbon-helix-helix	8090994	3000295	SCOP2B (2022-06-29)
A	SCOP2 Family	RelB antitoxin-like	8045581	4004546	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribbon-helix-helix	8090994	3000295	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	adh_short_C2	e4fxeD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: SH3	T: SH3	F: adh_short_C2	ECOD (v294.1)
F	Nuc_deoxyrib_tr	e4fxeF3	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Nuc_deoxyrib_tr	ECOD (v294.1)
E	tRNA_synthFbeta	e4fxeE2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: tRNA_synthFbeta	ECOD (v294.1)
B	Rrf2	e4fxeB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: Rrf2	ECOD (v294.1)
C	SH3_16	e4fxeC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SH3_16	ECOD (v294.1)
A	RelB	e4fxeA1	A: a/b three-layered sandwiches	X: Baculovirus p35 protein-related	H: Baculovirus p35 protein-related	T: Ribbon-helix-helix	F: RelB	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
E	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
B	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
C	6.10.250.2570	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, E, F	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
D, E, F	mRNA interferase RelE	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding RNA binding rRNA binding molecular sequestering activity toxin sequestering activity ribonucleoprotein complex binding protein-containing complex binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding RNA binding rRNA binding molecular sequestering activity toxin sequestering activity ribonucleoprotein complex binding protein-containing complex binding ribosome 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 hydrolase activity transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary 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 metabolic process cellular process macromolecule metabolic process regulation of metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription catabolic process macromolecule catabolic process RNA catabolic process mRNA catabolic process mRNA metabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process response to stimulus response to chemical response to antibiotic regulation of growth growth cellular response to stimulus response to nutrient levels cellular response to amino acid starvation cellular response to starvation cellular response to nutrient levels cellular response to stress response to stress response to amino acid starvation response to starvation cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms single-species biofilm formation aggregation of unicellular organisms	protein-containing complex transcription regulator complex toxin-antitoxin complex transcription repressor complex protein-DNA complex
A, B, C	Antitoxin RelB	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding molecular sequestering activity toxin sequestering activity transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity	regulation of growth regulation of biological process biological regulation growth regulation of cellular 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of growth regulation of biological process biological regulation growth regulation of cellular 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms single-species biofilm formation aggregation of unicellular organisms	protein-containing complex transcription regulator complex toxin-antitoxin complex transcription repressor complex protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, E, F	IPR007712	Toxin-antitoxin system, RelE/ParE toxin family	Family
D, E, F	IPR035093	Toxin-antitoxin system, RelE/ParE toxin domain superfamily	Homologous Superfamily
A, B, C	IPR013321	Arc-type ribbon-helix-helix	Homologous Superfamily
A, B, C	IPR007337	RelB antitoxin/Antitoxin DinJ	Family

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.