2A6Q

Crystal structure of YefM-YoeB complex

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	d2a6qa1	Alpha and beta proteins (a+b)	YefM-like	YefM-like	YefM-like	Antitoxin YefM	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2a6qa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2a6qb1	Alpha and beta proteins (a+b)	YefM-like	YefM-like	YefM-like	Antitoxin YefM	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2a6qb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2a6qc2	Alpha and beta proteins (a+b)	YefM-like	YefM-like	YefM-like	Antitoxin YefM	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2a6qc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2a6qd2	Alpha and beta proteins (a+b)	YefM-like	YefM-like	YefM-like	Antitoxin YefM	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2a6qd3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2a6qe1	Alpha and beta proteins (a+b)	RelE-like	RelE-like	YoeB/Txe-like	Toxin YoeB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2a6qf_	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	SCOP2 Family	YefM-like	8024298	4003460	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YefM-like	8036677	3000907	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	YefM-like	8036677	3000907	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YefM-like	8036677	3000907	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	YefM-like	8036677	3000907	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	PhdYeFM_antitox	e2a6qA1	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	PhdYeFM_antitox	e2a6qB1	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)
C	PhdYeFM_antitox	e2a6qC2	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_1	e2a6qD1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PhdYeFM_antitox_1	ECOD (1.6)
E	YoeB_toxin	e2a6qE1	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	e2a6qF1	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	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
A	6.10.250.330	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
C	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
C	6.10.250.330	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		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)
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	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
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	Antitoxin yefM	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity toxic substance binding sequence-specific DNA binding DNA binding nucleic acid binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of growth growth 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
E, F	Toxin yoeB	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity 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 identical protein binding protein binding binding protein homodimerization activity protein dimerization activity 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 nucleic acid binding endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters RNA endonuclease activity, producing 3'-phosphomonoesters 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 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	IPR006442	Type II toxin-antitoxin system, antitoxin Phd/YefM	Family
A, B, C, D	IPR051405	phD/YefM antitoxin	Family
A, B, C, D	IPR036165	YefM-like superfamily	Homologous Superfamily
E, F	IPR035093	Toxin-antitoxin system, RelE/ParE toxin domain superfamily	Homologous Superfamily
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.