7V6W | pdb_00007v6w

Crystal structure of heterohexameric Sa2YoeB-Sa2YefM complex bound to 26bp-DNA

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L [auth J]	PhdYeFM_antitox	e7v6wJ1	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)
K [auth D]	PhdYeFM_antitox	e7v6wD1	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)
I [auth K]	PhdYeFM_antitox	e7v6wK1	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)
H [auth I]	PhdYeFM_antitox	e7v6wI1	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)
G [auth L]	PhdYeFM_antitox	e7v6wL1	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 [auth A]	PhdYeFM_antitox	e7v6wA1	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	e7v6wC1	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	e7v6wB1	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)
J [auth N]	ParE_toxin_1	e7v6wN1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: ParE_toxin_1	ECOD (1.6)
F [auth M]	ParE_toxin_1	e7v6wM1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: ParE_toxin_1	ECOD (1.6)
E	ParE_toxin_1	e7v6wE1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: ParE_toxin_1	ECOD (1.6)
A [auth F]	ParE_toxin_1	e7v6wF1	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)
I [auth K]	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (utative)
H [auth I]	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (utative)
D [auth A]	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (utative)
C	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, C, D [auth A], G [auth L], H [auth I], B, C, D [auth A], G [auth L], H [auth I], I [auth K], K [auth D], L [auth J]	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
A [auth F], E, F [auth M], J [auth N]	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
N [auth H], O [auth P]	DNA (25-MER)	-	-	-
M [auth G], P [auth O]	DNA (26-MER)	-	-	-
B, C, D [auth A], G [auth L], H [auth I], B, C, D [auth A], G [auth L], H [auth I], I [auth K], K [auth D], L [auth J]	Antitoxin	transcription regulator activity DNA-binding transcription factor activity sequence-specific DNA binding DNA binding binding nucleic acid 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	-
A [auth F], E, F [auth M], J [auth N]	Putative mRNA interferase YoeB	hydrolase activity catalytic activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid	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 catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, C, D [auth A], G [auth L], H [auth I], B, C, D [auth A], G [auth L], H [auth I], I [auth K], K [auth D], L [auth J]	IPR006442	Type II toxin-antitoxin system, antitoxin Phd/YefM	Family
B, C, D [auth A], G [auth L], H [auth I], B, C, D [auth A], G [auth L], H [auth I], I [auth K], K [auth D], L [auth J]	IPR051405	phD/YefM antitoxin	Family
B, C, D [auth A], G [auth L], H [auth I], B, C, D [auth A], G [auth L], H [auth I], I [auth K], K [auth D], L [auth J]	IPR036165	YefM-like superfamily	Homologous Superfamily
A [auth F], E, F [auth M], J [auth N]	IPR009614	Toxin YoeB	Family
A [auth F], E, F [auth M], J [auth N]	IPR035093	Toxin-antitoxin system, RelE/ParE toxin domain superfamily	Homologous Superfamily

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.