4ML0

Crystal structure of E.coli DinJ-YafQ 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)
B	d4ml0b_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli B str. REL606 ) [TaxId: 413997 ],	SCOPe (2.08)
D	d4ml0d_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli B str. REL606 ) [TaxId: 413997 ],	SCOPe (2.08)
F	d4ml0f_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli B str. REL606 ) [TaxId: 413997 ],	SCOPe (2.08)
H	d4ml0h_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli B str. REL606 ) [TaxId: 413997 ],	SCOPe (2.08)
J	d4ml0j_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli B str. REL606 ) [TaxId: 413997 ],	SCOPe (2.08)
L	d4ml0l_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli B str. REL606 ) [TaxId: 413997 ],	SCOPe (2.08)
N	d4ml0n_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli B str. REL606 ) [TaxId: 413997 ],	SCOPe (2.08)
P	d4ml0p_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Escherichia coli B str. REL606 ) [TaxId: 413997 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribbon-helix-helix	8094265	3000295	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribbon-helix-helix	8094265	3000295	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribbon-helix-helix	8094265	3000295	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ribbon-helix-helix	8094265	3000295	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ribbon-helix-helix	8094265	3000295	SCOP2B (2022-06-29)
K	SCOP2 Family	RelB antitoxin-like	8094264	4004546	SCOP2 (2022-06-29)
K	SCOP2 Superfamily	Ribbon-helix-helix	8094265	3000295	SCOP2 (2022-06-29)
M	SCOP2B Superfamily	Ribbon-helix-helix	8094265	3000295	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Ribbon-helix-helix	8094265	3000295	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RelE-like	8063332	3000741	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RelE-like	8063332	3000741	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RelE-like	8063332	3000741	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RelE-like	8063332	3000741	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	RelE-like	8063332	3000741	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	RelE-like	8063332	3000741	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	RelE-like	8063332	3000741	SCOP2B (2022-06-29)
P	SCOP2 Family	RelE-like	8063331	4003388	SCOP2 (2022-06-29)
P	SCOP2 Superfamily	RelE-like	8063332	3000741	SCOP2 (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	RelB	e4ml0A1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
C	RelB	e4ml0C1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
E	RelB	e4ml0E1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
G	RelB	e4ml0G1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
I	RelB	e4ml0I1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
K	RelB	e4ml0K1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
M	RelB	e4ml0M1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
O	RelB	e4ml0O1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RelB	ECOD (1.6)
B	YafQ_toxin	e4ml0B1	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	e4ml0D1	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	e4ml0F1	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	e4ml0H1	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	e4ml0J1	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	e4ml0L1	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	e4ml0N1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YafQ_toxin	ECOD (1.6)
P	YafQ_toxin	e4ml0P1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YafQ_toxin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K, M, O	Predicted antitoxin of YafQ-DinJ toxin-antitoxin system	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding toxic substance 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 cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms single-species biofilm formation aggregation of unicellular organisms	-
B, D, F, H, J B, D, F, H, J, L, N, P	Predicted toxin of the YafQ-DinJ toxin-antitoxin system	DNA binding binding nucleic acid binding 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	cellular component disassembly protein-containing complex organization protein-containing complex disassembly primary metabolic process translation gene expression macromolecule biosynthetic process cellular component organization biosynthetic process cellular process metabolic process translational termination cellular component organization or biogenesis protein metabolic process cellular component disassembly protein-containing complex organization protein-containing complex disassembly primary metabolic process translation gene expression macromolecule biosynthetic process cellular component organization biosynthetic process cellular process metabolic process translational termination cellular component organization or biogenesis protein metabolic process macromolecule metabolic process regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic 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 mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
A, C, E, G, I A, C, E, G, I, K, M, O	IPR007337	RelB antitoxin/Antitoxin DinJ	Family
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	IPR004386	Toxin-antitoxin system, YafQ-like toxin	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

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.