4RUL | pdb_00004rul

Crystal structure of full-length E.Coli topoisomerase I in complex with ssDNA

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	Toprim domain-like	8055743	3000737	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Zinc beta-ribbon	8039157	3001238	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Prokaryotic type I DNA topoisomerase clamp domain-like	8036554	3001789	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)
A	TOP1_ZnF	e4rulA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: TOP1_ZnF	ECOD (v294.1)
A	H-kinase_dim	e4rulA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: H-kinase_dim	ECOD (v294.1)
A	XPG_N,XPG_I	e4rulA4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: XPG_N,XPG_I	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.140	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	1.10.460.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	domain 2	CATH (4.3.0)
A	2.70.20.10	Mainly Beta	Distorted Sandwich	Topoisomerase I	domain 3	CATH (4.3.0)
A	1.10.290.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21372	Topoisomerase I, zinc finger (Zn_ribbon_bTOP1)	Topoisomerase I, zinc finger	This entry represents a zinc ribbon domain found at the C-terminal of topoisomerase I from bacteria (it corresponds to D6 described in [1]. Topoisomerase I has an essential function in preventing hypernegative supercoiling of DNA. The C-terminal doma ...	This entry represents a zinc ribbon domain found at the C-terminal of topoisomerase I from bacteria (it corresponds to D6 described in [1]. Topoisomerase I has an essential function in preventing hypernegative supercoiling of DNA. The C-terminal domains bind ssDNA to recognise the accumulation of negative supercoils in duplex DNA [1].	Domain
A	PF01396	Topoisomerase DNA binding C4 zinc finger (Zn_ribbon_Top1)	Topoisomerase DNA binding C4 zinc finger		Domain
A	PF01131	DNA topoisomerase (Topoisom_bac)	DNA topoisomerase	-	Family
A	PF08272	Topoisomerase I zinc-ribbon-like (Zn_Ribbon_Topo)	Topoisomerase I zinc-ribbon-like	Some Proteobacteria topoisomerase I contain two zinc-ribbon-like domains at the C-terminus that structurally homologous to Pfam:PF01396. However, this domain no longer bind zinc. Indeed, only one of the four cysteine residues remains [1].	Domain
A	PF01751	Toprim domain (Toprim)	Toprim domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA topoisomerase 1	DNA binding binding nucleic acid binding RNA topoisomerase activity nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid macromolecular conformation isomerase activity catalytic activity DNA topoisomerase type I (single strand cut, ATP-independent) activity catalytic activity, acting on DNA DNA topoisomerase activity cation binding DNA binding binding nucleic acid binding RNA topoisomerase activity nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid macromolecular conformation isomerase activity catalytic activity DNA topoisomerase type I (single strand cut, ATP-independent) activity catalytic activity, acting on DNA DNA topoisomerase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular process cell cycle chromosome segregation cell cycle process chromosome organization primary metabolic process DNA conformation change DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process DNA topological change organelle organization metabolic process cellular process cell cycle chromosome segregation cell cycle process chromosome organization primary metabolic process DNA conformation change DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process DNA topological change organelle organization metabolic process cellular component organization or biogenesis macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromosome
B	single strand DNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR013498	DNA topoisomerase, type IA, zn finger	Domain
A	IPR003601	DNA topoisomerase, type IA, domain 2	Domain
A	IPR028612	DNA topoisomerase I, type IA	Family
A	IPR000380	DNA topoisomerase, type IA	Family
A	IPR013826	DNA topoisomerase, type IA, central region, subdomain 3	Homologous Superfamily
A	IPR006171	TOPRIM domain	Domain
A	IPR005733	DNA topoisomerase I, bacterial-type	Family
A	IPR013497	DNA topoisomerase, type IA, central	Domain
A	IPR003602	DNA topoisomerase, type IA, DNA-binding domain	Domain
A	IPR049330	Topoisomerase I, zinc finger	Domain
A	IPR013263	DNA topoisomerase I, zinc ribbon-like, bacterial-type	Domain
A	IPR023405	DNA topoisomerase, type IA, core domain	Homologous Superfamily
A	IPR013825	DNA topoisomerase, type IA, central region, subdomain 2	Homologous Superfamily
A	IPR023406	DNA topoisomerase, type IA, active site	Active Site
A	IPR034149	DNA topoisomerase 1, TOPRIM domain	Domain
A	IPR013824	DNA topoisomerase, type IA, central region, subdomain 1	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.