4ME7 | pdb_00004me7

Crystal structure of Bacillus subtilis toxin MazF in complex with cognate antitoxin MazE

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)
D	d4me7d1	All beta proteins	SH3-like barrel	Cell growth inhibitor/plasmid maintenance toxic component	Kid/PemK	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
D	d4me7d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
C	d4me7c1	All beta proteins	SH3-like barrel	Cell growth inhibitor/plasmid maintenance toxic component	Kid/PemK	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
C	d4me7c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
B	d4me7b1	All beta proteins	SH3-like barrel	Cell growth inhibitor/plasmid maintenance toxic component	Kid/PemK	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
B	d4me7b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
A	d4me7a1	All beta proteins	SH3-like barrel	Cell growth inhibitor/plasmid maintenance toxic component	Kid/PemK	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
A	d4me7a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Cell growth inhibitor/plasmid maintenance toxic component	8043762	3000352	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cell growth inhibitor/plasmid maintenance toxic component	8043762	3000352	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cell growth inhibitor/plasmid maintenance toxic component	8043762	3000352	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cell growth inhibitor/plasmid maintenance toxic component	8043762	3000352	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)
D	PemK_toxin	e4me7D1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PemK_toxin	ECOD (1.6)
C	PemK_toxin	e4me7C1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PemK_toxin	ECOD (1.6)
B	PemK_toxin	e4me7B1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PemK_toxin	ECOD (1.6)
A	PemK_toxin	e4me7A1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PemK_toxin	ECOD (1.6)
F	RHH_1	e4me7F1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RHH_1	ECOD (1.6)
E	RHH_1	e4me7E1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RHH_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.30.30.110	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C	2.30.30.110	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	2.30.30.110	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	2.30.30.110	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
F	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
E	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
A, B, C, D	PF02452	PemK-like, MazF-like toxin of type II toxin-antitoxin system (PemK_toxin)	PemK-like, MazF-like toxin of type II toxin-antitoxin system	PemK is a growth inhibitor in E. coli known to bind to the promoter region of the Pem operon, auto-regulating synthesis. This family represents the toxin molecule of a typical bacterial toxin-antitoxin system pairing. The family includes a number of ...	PemK is a growth inhibitor in E. coli known to bind to the promoter region of the Pem operon, auto-regulating synthesis. This family represents the toxin molecule of a typical bacterial toxin-antitoxin system pairing. The family includes a number of different toxins, such as MazF, Kid, PemK, ChpA, ChpB and ChpAK.	Domain
E, F	PF01402	Ribbon-helix-helix protein, copG family (RHH_1)	Ribbon-helix-helix protein, copG family	The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement [2]. The helix-turn-helix-like structure is involved in dimerisation and not DNA b ...	The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement [2]. The helix-turn-helix-like structure is involved in dimerisation and not DNA binding as might have been expected [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	mRNA interferase EndoA	DNA binding binding nucleic acid 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 RNA binding	catabolic process RNA metabolic process primary metabolic process rRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process rRNA metabolic process RNA catabolic process catabolic process RNA metabolic process primary metabolic process rRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process rRNA metabolic process RNA catabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process	-
E, F	Antitoxin EndoAI	identical protein binding protein binding 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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR011067	Plasmid maintenance toxin/Cell growth inhibitor	Homologous Superfamily
A, B, C, D	IPR003477	mRNA interferase PemK-like	Family
E, F	IPR013321	Arc-type ribbon-helix-helix	Homologous Superfamily
E, F	IPR010985	Ribbon-helix-helix	Homologous Superfamily
E, F	IPR002145	Ribbon-helix-helix protein, CopG	Domain

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.