› 6cq2

X-ray diffraction
3Å resolution

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

Released:
DOI: 10.2210/pdb6cq2/pdb
PDB entry 6cq2 coloured by chain, front view.
PDB entry 6cq2 coloured by chain, side view.
PDB entry 6cq2 coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site.
Cao N, Tan K, Annamalai T, Joachimiak A, Tse-Dinh YC
Nucleic Acids Res 46 7296-7308 (2018)
PMID: 29905859

Function and Biology Details

Reaction catalysed: 
ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119677 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA topoisomerase 1 Chain: A
Molecule details ›
Chain: A
Length: 706 amino acids
Theoretical weight: 77.84 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli
UniProt:
  • Canonical: P9WG49 (Residues: 2-704; Coverage: 75%)
Gene names: MTCY15C10.06, Rv3646c, topA
Sequence domains:
Structure domains:
DNA (5'-D(P*TP*TP*CP*CP*GP*CP*TP*TP*GP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 3.91 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 4 x MG
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 67.625Å b: 44.683Å c: 128.866Å
α: 90° β: 90.61° γ: 90°
R-values:
R R work R free
0.192 0.188 0.249
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Unravelling the mechanisms of Type 1A topoisomerases using single-molecule approaches.
Spakman et al. (2021)
2 more

3 mentions without citation

Mechanism of Type IA Topoisomerases.
Dasgupta et al. (2020)
2 more