2A6R | pdb_00002a6r

Crystal structure of YoeB under PEG condition

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)
A	d2a6ra_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	YoeB/Txe-like	Toxin YoeB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2a6rb_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	YoeB/Txe-like	Toxin YoeB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2a6rc_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	YoeB/Txe-like	Toxin YoeB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2a6rd_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	YoeB/Txe-like	Toxin YoeB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2a6re_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	YoeB/Txe-like	Toxin YoeB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2a6rf_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	YoeB/Txe-like	Toxin YoeB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RelE-like	8036678	3000741	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RelE-like	8036678	3000741	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RelE-like	8036678	3000741	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RelE-like	8036678	3000741	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RelE-like	8036678	3000741	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RelE-like	8036678	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)
A	YoeB_toxin	e2a6rA1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YoeB_toxin	ECOD (1.6)
B	YoeB_toxin	e2a6rB1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YoeB_toxin	ECOD (1.6)
C	YoeB_toxin	e2a6rC1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YoeB_toxin	ECOD (1.6)
D	YoeB_toxin	e2a6rD1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YoeB_toxin	ECOD (1.6)
E	YoeB_toxin	e2a6rE1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YoeB_toxin	ECOD (1.6)
F	YoeB_toxin	e2a6rF1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YoeB_toxin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
C	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)
E	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF06769	YoeB-like toxin of bacterial type II toxin-antitoxin system (YoeB_toxin)	YoeB-like toxin of bacterial type II toxin-antitoxin system	YoeB_toxin is a family of bacterial toxins that forms one component of the type II toxin-antitoxin system in E. coli whose antitoxin is represented by YefM, found in Pfam:PF02604. The plasmid encoded Axe-Txe proteins in Enterococcus faecium act as a ...	YoeB_toxin is a family of bacterial toxins that forms one component of the type II toxin-antitoxin system in E. coli whose antitoxin is represented by YefM, found in Pfam:PF02604. The plasmid encoded Axe-Txe proteins in Enterococcus faecium act as an antitoxin-toxin pair. When the plasmid is lost, the antitoxin is degraded relatively quickly by host enzymes. This allows the toxin to interact with its intracellular target, thus killing the cell or impeding cell growth [1]. These toxins are highly potent protein synthesis inhibitors, specifically blocking the initiation of translation. In the case of YoeB, it binds to the 50 S ribosomal subunit in 70 S ribosomes and interacts with the A site leading to mRNA cleavage at this site. As a result, the 3'-end portion of the mRNA is released from ribosomes, and translation initiation is effectively inhibited [2,3].	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	Toxin yoeB	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity 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 nucleic acid binding identical protein binding protein binding binding protein homodimerization activity protein dimerization activity 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 nucleic acid binding RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism hydrolase activity, acting on ester bonds hydrolase activity ribonucleoprotein complex binding protein-containing complex binding ribosomal small subunit binding ribosome binding	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 regulation of biological process biological regulation primary metabolic process 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 regulation of biological process biological regulation 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 catabolic process negative regulation of biological process macromolecule catabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process mRNA catabolic process negative regulation of metabolic process mRNA metabolic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process post-transcriptional regulation of gene expression global gene silencing by mRNA cleavage post-transcriptional gene silencing protein biosynthetic process negative regulation of translation translational initiation protein metabolic process negative regulation of protein metabolic process regulation of translational initiation regulation of protein metabolic process negative regulation of translational initiation translation regulation of translation regulation of growth growth response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR035093	Toxin-antitoxin system, RelE/ParE toxin domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR009614	Toxin YoeB	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.