3NFC | pdb_00003nfc

Crystal structure of E.coli MazF Toxin

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)
F	d3nfcf_	All beta proteins	SH3-like barrel	Cell growth inhibitor/plasmid maintenance toxic component	Kid/PemK	MazF protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E	d3nfce_	All beta proteins	SH3-like barrel	Cell growth inhibitor/plasmid maintenance toxic component	Kid/PemK	MazF protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d3nfcd_	All beta proteins	SH3-like barrel	Cell growth inhibitor/plasmid maintenance toxic component	Kid/PemK	MazF protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3nfcc_	All beta proteins	SH3-like barrel	Cell growth inhibitor/plasmid maintenance toxic component	Kid/PemK	MazF protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3nfcb_	All beta proteins	SH3-like barrel	Cell growth inhibitor/plasmid maintenance toxic component	Kid/PemK	MazF protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3nfca_	All beta proteins	SH3-like barrel	Cell growth inhibitor/plasmid maintenance toxic component	Kid/PemK	MazF protein	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Cell growth inhibitor/plasmid maintenance toxic component	8034895	3000352	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cell growth inhibitor/plasmid maintenance toxic component	8034895	3000352	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cell growth inhibitor/plasmid maintenance toxic component	8034895	3000352	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cell growth inhibitor/plasmid maintenance toxic component	8034895	3000352	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cell growth inhibitor/plasmid maintenance toxic component	8034895	3000352	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cell growth inhibitor/plasmid maintenance toxic component	8034895	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)
F	YjeF_N	e3nfcF1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
E	YjeF_N	e3nfcE1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
D	YjeF_N	e3nfcD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
C	YjeF_N	e3nfcC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
B	YjeF_N	e3nfcB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
A	Anemone_cytotox	e3nfcA1	A: a/b three-layered sandwiches	X: EF-hand	H: Insect pheromone/odorant-binding proteins	T: Insect pheromone/odorant-binding proteins	F: Anemone_cytotox	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.30.30.110	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
E	2.30.30.110	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	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

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	PemK-like protein 1	DNA binding binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity protein-containing complex binding endonuclease activity nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity DNA binding binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity protein-containing complex 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 molecular function activator activity molecular function regulator activity hydrolase activity RNA 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 positive regulation of programmed cell death positive regulation of biological process regulation of programmed cell death cell death programmed cell death positive regulation of cellular process response to stimulus signaling quorum sensing cell-cell signaling detection of cell density detection of biotic stimulus response to biotic stimulus cell communication detection of stimulus regulation of growth growth regulation of protein metabolic process translation protein biosynthetic process post-transcriptional regulation of gene expression regulation of translation protein metabolic process rRNA catabolic process rRNA metabolic process regulation of cellular component organization negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth cellular component organization or biogenesis biological process involved in interspecies interaction between organisms defense response to virus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus 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	IPR011067	Plasmid maintenance toxin/Cell growth inhibitor	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR003477	mRNA interferase PemK-like	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.