5HY3

Crystal structure of Escherichia coli toxin LsoA in complex with T4 phage antitoxin Dmd

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	SCOP2 Family	RNase LS-like	8044769	4004123	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TT1751-like	8052562	3001862	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HEPN domain-like	8052561	3000904	SCOP2 (2022-06-29)
B	SCOP2 Family	Dmd-like	8047137	4005464	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Dmd-like	8052563	3002128	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	PF19034	e5hy3A1	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: PF19034	ECOD (1.6)
A	PF15935	e5hy3A2	A: a+b two layers	X: TBP-like	H: Toxin RnlA N-terminal domains (From Topology)	T: Toxin RnlA N-terminal domains	F: PF15935	ECOD (1.6)
B	PF17587	e5hy3B1	A: a+b two layers	X: GTP-binding protein lepA C-terminal domain-like	H: Antitoxin Dmd (From Topology)	T: Antitoxin Dmd	F: PF17587	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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
B	PF17587	Discriminator of mRNA degradation (Dmd)	Discriminator of mRNA degradation	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	mRNA endoribonuclease LsoA	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	-	-
B	Antitoxin Dmd	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR043994	Bacterial toxin, RNase RnlA/LsoA, DBD domain	Domain
A	IPR031845	Bacterial toxin, RNase RnlA/LsoA, N-terminal repeated domain	Domain
A	IPR045837	Bacterial toxin, RNase RnlA/LsoA, N-terminal	Domain
B	IPR035137	Discriminator of mRNA degradation	Family

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.