4I8O

Crystal structure of the toxin RnlA from Escherichia coli

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	TT1751-like	8052560	3001862	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TT1751-like	8052558	3001862	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HEPN domain-like	8052557	3000904	SCOP2B (2022-06-29)
B	SCOP2 Family	RNase LS-like	8044768	4004123	SCOP2 (2022-06-29)
B	SCOP2 Family	RnlA N-terminal domain-like	8052559	4007593	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	TT1751-like	8052558	3001862	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	TT1751-like	8052560	3001862	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	HEPN domain-like	8052557	3000904	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	RnlA_toxin_C	e4i8oA3	A: alpha bundles	X: Toxin RnlA C-terminal domain (From Topology)	H: Toxin RnlA C-terminal domain (From Topology)	T: Toxin RnlA C-terminal domain	F: RnlA_toxin_C	ECOD (1.6)
A	RnlA_toxin_N	e4i8oA2	A: a+b two layers	X: TBP-like	H: Toxin RnlA N-terminal domains (From Topology)	T: Toxin RnlA N-terminal domains	F: RnlA_toxin_N	ECOD (1.6)
A	RNLA_N_1	e4i8oA1	A: a+b two layers	X: TBP-like	H: Toxin RnlA N-terminal domains (From Topology)	T: Toxin RnlA N-terminal domains	F: RNLA_N_1	ECOD (1.6)
B	RnlA_toxin_C	e4i8oB1	A: alpha bundles	X: Toxin RnlA C-terminal domain (From Topology)	H: Toxin RnlA C-terminal domain (From Topology)	T: Toxin RnlA C-terminal domain	F: RnlA_toxin_C	ECOD (1.6)
B	RnlA_toxin_N	e4i8oB3	A: a+b two layers	X: TBP-like	H: Toxin RnlA N-terminal domains (From Topology)	T: Toxin RnlA N-terminal domains	F: RnlA_toxin_N	ECOD (1.6)
B	RNLA_N_1	e4i8oB2	A: a+b two layers	X: TBP-like	H: Toxin RnlA N-terminal domains (From Topology)	T: Toxin RnlA N-terminal domains	F: RNLA_N_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.310.240	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	Bacterial toxin RNase RnlA/LsoA, N-terminal domain	CATH (4.3.0)
A	3.30.160.690	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Bacterial toxin RNase RnlA/LsoA, N repeated domain	CATH (4.3.0)
A	1.10.8.1130	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	6.10.250.2650	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	3.30.310.240	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	Bacterial toxin RNase RnlA/LsoA, N-terminal domain	CATH (4.3.0)
B	3.30.160.690	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Bacterial toxin RNase RnlA/LsoA, N repeated domain	CATH (4.3.0)
B	1.10.8.1130	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	6.10.250.2650	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF15935	RNase LS, bacterial toxin (RnlA_toxin)	RNase LS, bacterial toxin	RnlA_toxin is an RNase LS and a putative toxin of a bacterial toxin-antitoxin pair. Toxin-antitoxin systems consist of a stable toxin and an unstable antitoxin. In this case, a novel type II system, RnlA is the stable toxin that causes inhibition of ...	RnlA_toxin is an RNase LS and a putative toxin of a bacterial toxin-antitoxin pair. Toxin-antitoxin systems consist of a stable toxin and an unstable antitoxin. In this case, a novel type II system, RnlA is the stable toxin that causes inhibition of cell growth and rapidly degrades T4 late mRNAs to prevent their expression, and this is neutralised by the activity of the unstable antitoxin RnlB [1, 2].	Domain
A, B	PF19034	RNase LS, bacterial toxin DBD domain (RnlA-toxin_DBD)	RNase LS, bacterial toxin DBD domain	RnlA toxin is an RNase LS and a putative toxin of a bacterial toxin-antitoxin pair. Toxin-antitoxin systems consist of a stable toxin and an unstable antitoxin. In this case, a novel type II system, RnlA is the stable toxin that causes inhibition of ...	RnlA toxin is an RNase LS and a putative toxin of a bacterial toxin-antitoxin pair. Toxin-antitoxin systems consist of a stable toxin and an unstable antitoxin. In this case, a novel type II system, RnlA is the stable toxin that causes inhibition of cell growth and rapidly degrades T4 late mRNAs to prevent their expression, and this is neutralised by the activity of the unstable antitoxin RnlB [1, 2]. This entry represents the C-terminal DBD domain, responsible for the RNA cleavage activity and toxicity. Through interaction between DBDs, RnlA dimerises in solution. T4 Dmd binds to DBD for inhibition of RnlA toxicity and RnlB also inhibits the toxicity of DBD [3].	Domain
A, B	PF19417	RNase LS, bacterial toxin N-terminal (RnlA_toxin_N)	RNase LS, bacterial toxin N-terminal	RnlA_toxin is an RNase LS and a putative toxin of a bacterial toxin-antitoxin pair. Toxin-antitoxin systems consist of a stable toxin and an unstable antitoxin. In this case, a novel type II system, RnlA is the stable toxin that causes inhibition of ...	RnlA_toxin is an RNase LS and a putative toxin of a bacterial toxin-antitoxin pair. Toxin-antitoxin systems consist of a stable toxin and an unstable antitoxin. In this case, a novel type II system, RnlA is the stable toxin that causes inhibition of cell growth and rapidly degrades T4 late mRNAs to prevent their expression, and this is neutralised by the activity of the unstable antitoxin RnlB [1, 2]. This entry represents the N-terminal domain composed of four-stranded twisted antiparallel beta-sheet and two alpha-helices [3,4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	TOXIN RNLA	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 identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	regulation of growth regulation of biological process biological regulation growth regulation of cellular process cellular biosynthetic 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 organic substance metabolic process regulation of growth regulation of biological process biological regulation growth regulation of cellular process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process catabolic process negative regulation of biological process negative regulation of cellular metabolic 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 negative regulation of cellular biosynthetic process organic cyclic compound catabolic 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 organic substance catabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus defense response to other organism response to stress 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 intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR043994	Bacterial toxin, RNase RnlA/LsoA, DBD domain	Domain
A, B	IPR031845	Bacterial toxin, RNase RnlA/LsoA, N-terminal repeated domain	Domain
A, B	IPR045837	Bacterial toxin, RNase RnlA/LsoA, N-terminal	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.