6PCM

Crystal Structure of Mycobacterium smegmatis Topoisomerase I with ssDNA bound to both N- and C-terminal domains

External Resource: Annotation

Domain Annotation: ECOD Classification
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	Topoisom_bac_2nd	e6pcmA4	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: Topoisom_bac_2nd	ECOD (1.6)
A	Topoisom_bac_3rd	e6pcmA2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Topoisom_bac_3rd	ECOD (1.6)
A	Topoisom_bac_1st	e6pcmA3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Topoisom_bac_1st	ECOD (1.6)
A	Toprim	e6pcmA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim	ECOD (1.6)
A	Toprim_C_rpt	e6pcmA6	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: Toprim_C_rpt	ECOD (1.6)
B	Topoisom_bac_2nd	e6pcmB5	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: Topoisom_bac_2nd	ECOD (1.6)
B	Topoisom_bac_3rd	e6pcmB3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Topoisom_bac_3rd	ECOD (1.6)
B	Topoisom_bac_1st	e6pcmB2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Topoisom_bac_1st	ECOD (1.6)
B	Toprim	e6pcmB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim	ECOD (1.6)
B	Toprim_C_rpt	e6pcmB6	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: Toprim_C_rpt	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01131	DNA topoisomerase (Topoisom_bac)	DNA topoisomerase	-	Family
A, B	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, 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
A, B	DNA topoisomerase 1	DNA binding 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 cation binding ion binding metal ion binding small molecule binding	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 organic cyclic compound metabolic process organelle organization organic substance metabolic process cellular process metabolic process cellular component organization or biogenesis 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 organic cyclic compound metabolic process organelle organization organic substance metabolic process cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process	-
C, D	DNA (5'-D(PAPGPTPGPAPGPCPGPAPGPCPTPTPCPCPGPCPTPTPGPAPCPTPT)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR013497	DNA topoisomerase, type IA, central	Domain
A, B	IPR003602	DNA topoisomerase, type IA, DNA-binding domain	Domain
A, B	IPR023405	DNA topoisomerase, type IA, core domain	Homologous Superfamily
A, B	IPR013825	DNA topoisomerase, type IA, central region, subdomain 2	Homologous Superfamily
A, B	IPR003601	DNA topoisomerase, type IA, domain 2	Domain
A, B	IPR025589	Topoisomerase C-terminal repeat	Repeat
A, B	IPR028612	DNA topoisomerase I, type IA	Family
A, B	IPR000380	DNA topoisomerase, type IA	Family
A, B	IPR013826	DNA topoisomerase, type IA, central region, subdomain 3	Homologous Superfamily
A, B	IPR006171	TOPRIM domain	Domain
A, B	IPR023406	DNA topoisomerase, type IA, active site	Active Site
A, B	IPR005733	DNA topoisomerase I, bacterial-type	Family
A, B	IPR034149	DNA topoisomerase 1, TOPRIM domain	Domain
A, B	IPR013824	DNA topoisomerase, type IA, central region, subdomain 1	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.