4Q2U | pdb_00004q2u

Crystal structure of the E. coli DinJ-YafQ toxin-antitoxin 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)
P	d4q2up_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
N	d4q2un_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
L	d4q2ul_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
J	d4q2uj_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
H	d4q2uh_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F	d4q2uf_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d4q2ud_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4q2ub_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(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)
P	SCOP2B Superfamily	RelE-like	8063330	3000741	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	RelE-like	8063330	3000741	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	RelE-like	8063330	3000741	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	RelE-like	8063330	3000741	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RelE-like	8063330	3000741	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RelE-like	8063330	3000741	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RelE-like	8063330	3000741	SCOP2B (2022-06-29)
B	SCOP2 Family	RelE-like	8063329	4003388	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	RelE-like	8063330	3000741	SCOP2 (2022-06-29)
O	SCOP2B Superfamily	Ribbon-helix-helix	8090996	3000295	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Ribbon-helix-helix	8090996	3000295	SCOP2B (2022-06-29)
K	SCOP2 Family	RelB antitoxin-like	8045582	4004546	SCOP2 (2022-06-29)
K	SCOP2 Superfamily	Ribbon-helix-helix	8090996	3000295	SCOP2 (2022-06-29)
I	SCOP2B Superfamily	Ribbon-helix-helix	8090996	3000295	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ribbon-helix-helix	8090996	3000295	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribbon-helix-helix	8090996	3000295	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribbon-helix-helix	8090996	3000295	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribbon-helix-helix	8090996	3000295	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)
P	YafQ_toxin	e4q2uP1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YafQ_toxin	ECOD (1.6)
N	YafQ_toxin	e4q2uN1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YafQ_toxin	ECOD (1.6)
L	YafQ_toxin	e4q2uL1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YafQ_toxin	ECOD (1.6)
J	YafQ_toxin	e4q2uJ1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YafQ_toxin	ECOD (1.6)
H	YafQ_toxin	e4q2uH1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YafQ_toxin	ECOD (1.6)
F	YafQ_toxin	e4q2uF1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YafQ_toxin	ECOD (1.6)
D	YafQ_toxin	e4q2uD1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YafQ_toxin	ECOD (1.6)
B	YafQ_toxin	e4q2uB1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YafQ_toxin	ECOD (1.6)
O	RelB	e4q2uO1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
M	RelB	e4q2uM1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
K	RelB	e4q2uK1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
I	RelB	e4q2uI1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
G	RelB	e4q2uG1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
E	RelB	e4q2uE1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
C	RelB	e4q2uC1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
A	RelB	e4q2uA1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
N	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
L	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
J	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
H	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)
D	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L, N, P	PF15738	Bacterial toxin of type II toxin-antitoxin system, YafQ (YafQ_toxin)	Bacterial toxin of type II toxin-antitoxin system, YafQ	YafQ is a family of bacterial toxin ribonucleases of type II toxin-antitoxin systems. The E.coli gene is expressed from the dinB operon [1,2]. The cognate antitoxin for the E. coli protein is DinJ, in family RelB_antitoxin, Pfam:PF02604.	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	PF04221	RelB antitoxin (RelB)	RelB antitoxin	RelE and RelB form a toxin-antitoxin system. RelE represses translation, probably through binding ribosomes ([1], [2]). RelB stably binds RelE, presumably deactivating it.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L, N, P	mRNA interferase YafQ	DNA binding binding nucleic acid binding ribonucleoprotein complex binding protein-containing complex binding ribosome 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 DNA binding binding nucleic acid binding ribonucleoprotein complex binding protein-containing complex binding ribosome 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 RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism hydrolase activity, acting on ester bonds hydrolase activity	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 RNA catabolic process mRNA catabolic process mRNA metabolic process nucleobase-containing compound catabolic process negative regulation of gene expression nucleic acid catabolic process response to stimulus response to chemical response to antibiotic regulation of growth growth cellular component disassembly protein-containing complex organization protein-containing complex disassembly translation protein biosynthetic process cellular component organization translational termination cellular component organization or biogenesis protein metabolic process 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
A, C, E, G, I A, C, E, G, I, K, M, O	Antitoxin DinJ	DNA binding binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity toxic substance 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 DNA-templated transcription initiation DNA-templated transcription initiation negative regulation of DNA-templated transcription initiation 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L, N, P	IPR007712	Toxin-antitoxin system, RelE/ParE toxin family	Family
B, D, F, H, J B, D, F, H, J, L, N, P	IPR035093	Toxin-antitoxin system, RelE/ParE toxin domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P	IPR004386	Toxin-antitoxin system, YafQ-like toxin	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR007337	RelB antitoxin/Antitoxin DinJ	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR013321	Arc-type ribbon-helix-helix	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR026262	Antitoxin DinJ	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.