2O59 | pdb_00002o59

Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol pH 8.0

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)
D [auth B]	SCOP2B Superfamily	Prokaryotic type I DNA topoisomerase clamp domain-like	8033735	3001789	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Toprim domain-like	8055739	3000737	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Prokaryotic type I DNA topoisomerase clamp domain-like	8033735	3001789	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Toprim domain-like	8055739	3000737	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)
D [auth B]		e2o59B1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: HTHP	F:	ECOD (20:10:01)
C [auth A]		e2o59A1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: HTHP	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	3.40.50.140	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D [auth B]	1.10.460.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	domain 2	CATH (4.3.0)
D [auth B]	2.70.20.10	Mainly Beta	Distorted Sandwich	Topoisomerase I	domain 3	CATH (4.3.0)
D [auth B]	1.10.290.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	domain 4	CATH (4.3.0)
C [auth A]	3.40.50.140	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C [auth A]	1.10.460.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	domain 2	CATH (4.3.0)
C [auth A]	2.70.20.10	Mainly Beta	Distorted Sandwich	Topoisomerase I	domain 3	CATH (4.3.0)
C [auth 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
C [auth A], D [auth B]	PF01131	DNA topoisomerase (Topoisom_bac)	DNA topoisomerase	-	Family
C [auth A], D [auth B]	PF01751	Toprim domain (Toprim)	Toprim domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth A], D [auth B]	DNA topoisomerase 3	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleic acid conformation isomerase activity isomerase activity DNA topoisomerase type I (single strand cut, ATP-independent) activity catalytic activity, acting on DNA DNA topoisomerase activity catalytic activity, acting on a nucleic acid catalytic activity macromolecular conformation isomerase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleic acid conformation isomerase activity isomerase activity DNA topoisomerase type I (single strand cut, ATP-independent) activity catalytic activity, acting on DNA DNA topoisomerase activity catalytic activity, acting on a nucleic acid catalytic activity macromolecular conformation isomerase activity sequence-specific DNA binding DNA binding sequence-specific single stranded DNA binding single-stranded DNA binding nucleic acid binding	chromosome separation cellular process cell cycle chromosome segregation cell cycle process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress chromosome separation cellular process cell cycle chromosome segregation cell cycle process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process macromolecule metabolic process DNA repair DNA-templated DNA replication DNA replication chromosome organization DNA conformation change cellular component organization DNA topological change organelle organization cellular component organization or biogenesis DNA recombination	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle replication fork intracellular membraneless organelle chromosome cytoplasmic replication fork cytoplasm
A [auth C], B [auth D]	5'-D(CPGPCPAPAPCPTPT)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR013497	DNA topoisomerase, type IA, central	Domain
C [auth A], D [auth B]	IPR003602	DNA topoisomerase, type IA, DNA-binding domain	Domain
C [auth A], D [auth B]	IPR023405	DNA topoisomerase, type IA, core domain	Homologous Superfamily
C [auth A], D [auth B]	IPR013825	DNA topoisomerase, type IA, central region, subdomain 2	Homologous Superfamily
C [auth A], D [auth B]	IPR003601	DNA topoisomerase, type IA, domain 2	Domain
C [auth A], D [auth B]	IPR000380	DNA topoisomerase, type IA	Family
C [auth A], D [auth B]	IPR013826	DNA topoisomerase, type IA, central region, subdomain 3	Homologous Superfamily
C [auth A], D [auth B]	IPR006171	TOPRIM domain	Domain
C [auth A], D [auth B]	IPR005738	DNA topoisomerase III	Family
C [auth A], D [auth B]	IPR023406	DNA topoisomerase, type IA, active site	Active Site
C [auth A], D [auth B]	IPR034144	DNA topoisomerase 3-like, TOPRIM domain	Domain
C [auth A], D [auth B]	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.