6CQ2

Crystal structure of Mycobacterium tuberculosis Topoisomerase I in complex with oligonucleotide MTS2-12 and Magnesium

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	F_UNCLASSIFIED	e6cq2A3	A: beta barrels	X: LigT-like	H: Prokaryotic type I DNA topoisomerase beta-barrel domain (From Topology)	T: Prokaryotic type I DNA topoisomerase beta-barrel domain	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF01131	e6cq2A2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF01131	ECOD (1.6)
A	PF01751	e6cq2A1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: PF01751	ECOD (1.6)
A	PF13368	e6cq2A4	A: few secondary structure elements	X: Rubredoxin-like	H: Mycobacterium tuberculosis Topoisomerase I C-terminal domain (From Topology)	T: Mycobacterium tuberculosis Topoisomerase I C-terminal domain	F: PF13368	ECOD (1.6)

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	PF01131	DNA topoisomerase (Topoisom_bac)	DNA topoisomerase	-	Family
A	PF13368	Topoisomerase C-terminal repeat (Toprim_C_rpt)	Topoisomerase C-terminal repeat	This domain is repeated up to five times to form the C-terminal region of bacterial topoisomerase immediately downstream of the zinc-finger motif.	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	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding organic cyclic compound binding nucleic acid binding 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 cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding organic cyclic compound binding nucleic acid binding 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	negative regulation of hydrolase activity regulation of ribonuclease activity regulation of catalytic activity negative regulation of biological process RNA metabolic process negative regulation of catalytic activity regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process organic substance metabolic process regulation of nuclease activity negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of hydrolase activity regulation of ribonuclease activity regulation of catalytic activity negative regulation of biological process RNA metabolic process negative regulation of catalytic activity regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process organic substance metabolic process regulation of nuclease activity negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of ribonuclease activity regulation of biological process negative regulation of metabolic process biological regulation negative regulation of molecular function primary metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process organic cyclic compound metabolic process regulation of molecular function regulation of hydrolase activity metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of RNA metabolic process negative regulation of nuclease activity chromosome organization DNA conformation change DNA metabolic process cellular component organization DNA topological change organelle organization cellular process cellular component organization or biogenesis	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall
B	DNA (5'-D(PTPTPCPCPGPCPTPTPGPA)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR013497	DNA topoisomerase, type IA, central	Domain
A	IPR003602	DNA topoisomerase, type IA, DNA-binding domain	Domain
A	IPR023405	DNA topoisomerase, type IA, core domain	Homologous Superfamily
A	IPR013825	DNA topoisomerase, type IA, central region, subdomain 2	Homologous Superfamily
A	IPR003601	DNA topoisomerase, type IA, domain 2	Domain
A	IPR025589	Topoisomerase C-terminal repeat	Repeat
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	IPR023406	DNA topoisomerase, type IA, active site	Active Site
A	IPR005733	DNA topoisomerase I, bacterial-type	Family
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 R01GM133198.