1V74 | pdb_00001v74

Structure of the E. coli colicin D bound to its immunity protein ImmD

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	d1v74b_	All alpha proteins	Four-helical up-and-down bundle	Colicin D immunity protein	Colicin D immunity protein	Colicin D immunity protein	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1v74a_	Alpha and beta proteins (a+b)	Colicin D/E5 nuclease domain	Colicin D/E5 nuclease domain	Colicin D nuclease domain	Colicin D nuclease domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Colicin D immunity protein	8023162	4000636	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Colicin D immunity protein	8035542	3000820	SCOP2 (2022-06-29)
A	SCOP2 Family	Colicin D nuclease domain	8023160	4001320	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Colicin D/E5 nuclease domain	8035540	3001283	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)
B	Colicin_immun	e1v74B1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Colicin D immunity protein (From Topology)	T: Colicin D immunity protein	F: Colicin_immun	ECOD (1.6)
A	Colicin_D	e1v74A1	A: a+b two layers	X: Microbial ribonucleases-like	H: Colicin D nuclease domain (From Topology)	T: Colicin D nuclease domain	F: Colicin_D	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.20.120.650	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Colicin D	CATH (4.3.0)
A	3.10.450.200	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF09204	Bacterial self-protective colicin-like immunity (Colicin_immun)	Bacterial self-protective colicin-like immunity	Colicin D, which is synthesised by various prokaryotes, adopts an antiparallel four helical bundle fold: the helices are tightly packed, forming a compact cylindrical molecule. The protein specifically cleaves the anticodon loop of all four tRNA-Arg ...	Colicin D, which is synthesised by various prokaryotes, adopts an antiparallel four helical bundle fold: the helices are tightly packed, forming a compact cylindrical molecule. The protein specifically cleaves the anticodon loop of all four tRNA-Arg isoacceptors, thereby inactivating prokaryotic protein synthesis and leading to cell death [1]. This family also contains immunity proteins to klebicins and microcins. Many bacteria produce proteins that destroy their competitors. Colicin D is one such. The immunity proteins are expressed on the same operon as their cognate bacteriocins and protect the expressing bacterium from the effects of its own bacteriocin [2].	Domain
A	PF11429	Colicin D (Colicin_D)	Colicin D	Colicin D is a tRNase which kills sensitive E.coli cells via a specific tRNA cleavage. It targets the four isoaccepting tRNAs for Arg and cleaves the phosphodiester bond between positions 38 and 39 at the 3' junction of the anticodon stem and the loo ...	Colicin D is a tRNase which kills sensitive E.coli cells via a specific tRNA cleavage. It targets the four isoaccepting tRNAs for Arg and cleaves the phosphodiester bond between positions 38 and 39 at the 3' junction of the anticodon stem and the loop [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Colicin D immunity protein	binding toxic substance binding	metabolic process cellular process bacteriocin immunity toxin metabolic process secondary metabolic process	-
A	Colicin D	nuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity	defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing	intracellular anatomical structure cellular anatomical structure extrachromosomal circular DNA extrachromosomal DNA

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR015287	Colicin D immunity protein domain	Domain
B	IPR036471	Colicin D superfamily	Homologous Superfamily
A	IPR024440	Colicin D, C-terminal	Domain
A	IPR024575	Cloacin/colicin	Family
A	IPR038233	Colicin D/E5 nuclease domain superfamily	Homologous Superfamily
A	IPR016128	Pyosin/cloacin translocation domain	Domain
A	IPR036302	Pyosin/cloacin translocation domain superfamily	Homologous Superfamily
A	IPR037178	Colicin D, C-terminal 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.