3M4A | pdb_00003m4a

Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PPC	e3m4aA1	A: a/b three-layered sandwiches	X: Globin-like	H: Globin-like	T: Globin-like	F: PPC	ECOD (v294.1)
A	Topoisom_I	e3m4aA6	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Topoisom_I	ECOD (v294.1)
A	NLPC_P60	e3m4aA7	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: NLPC_P60	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.66.10	Alpha Beta	2-Layer Sandwich	Viral Topoisomerase I	DNA topoisomerase I domain	CATH (4.3.0)
A	1.10.132.120	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)
A	3.90.15.10	Alpha Beta	Alpha-Beta Complex	Topoisomerase I	Chain A, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01028	Eukaryotic DNA topoisomerase I, catalytic core (Topoisom_I)	Eukaryotic DNA topoisomerase I, catalytic core	Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth E]	DNA (5'-D(GPCPGPCPCPCPTPTPAPTPTPC)-3')	-	-	-
B [auth D]	DNA (5'-D(GPAPAPTPAPAPGPGPGPCPGPC)-3')	-	-	-
A	Putative Type I topoisomerase	DNA binding binding nucleic acid 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	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 cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR035447	DNA topoisomerase I, N-terminal domain superfamily	Homologous Superfamily
A	IPR011010	DNA breaking-rejoining enzyme, catalytic core	Homologous Superfamily
A	IPR049331	DNA topoisomerase IB, N-terminal domain	Domain
A	IPR001631	DNA topoisomerase I	Family
A	IPR013500	DNA topoisomerase I, catalytic core, eukaryotic-type	Domain
A	IPR014711	DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type	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.