› 2b9s

X-ray diffraction
2.27Å resolution

Crystal Structure of heterodimeric L. donovani topoisomerase I-vanadate-DNA complex

Released:
DOI: 10.2210/pdb2b9s/pdb
PDB entry 2b9s coloured by chain, front view.
PDB entry 2b9s coloured by chain, side view.
PDB entry 2b9s coloured by chain, top view.
Source organism: Leishmania donovani
Primary publication:
The structure of the transition state of the heterodimeric topoisomerase I of Leishmania donovani as a vanadate complex with nicked DNA.
Davies DR, Mushtaq A, Interthal H, Champoux JJ, Hol WG
J Mol Biol 357 1202-10 (2006)
PMID: 16487540

Function and Biology Details

Reaction catalysed: 
ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115105 (preferred)
Entry contents:
2 distinct polypeptide molecules
3 distinct DNA molecules
Macromolecules (5 distinct):
DNA topoisomerase I Chain: A
Molecule details ›
Chain: A
Length: 432 amino acids
Theoretical weight: 50.9 KDa
Source organism: Leishmania donovani
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9GPZ9 (Residues: 25-456; Coverage: 68%)
Gene name: LINJ_34_3220
Sequence domains:
Structure domains:
Topoisomerase I C-terminal domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 62 amino acids
Theoretical weight: 7.14 KDa
Source organism: Leishmania donovani
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8WQM6 (Residues: 201-262; Coverage: 24%)
Sequence domains: C-terminal topoisomerase domain
5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.06 KDa
5'-D(*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3' Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.68 KDa
5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3' Chain: E
Molecule details ›
Chain: E
Length: 22 nucleotides
Theoretical weight: 6.71 KDa

Ligands and Environments

1 bound ligand:
Ligand VO4 1 x VO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P212121
Unit cell:
a: 72.433Å b: 106.102Å c: 126.691Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.231 0.275
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

9 review citations

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
8 more

14 mentions without citation

16alpha-Hydroxycleroda-3,13 (14)Z-dien-15,16-olide from Polyalthia longifolia: a safe and orally active antileishmanial agent.
Misra et al. (2010)
13 more