3M6K

Crystal Structure of N-terminal 44 kDa fragment of topoisomerase V in the presence of guanidium hydrochloride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of minimal catalytic fragments of topoisomerase v reveals conformational changes relevant for DNA binding.

Rajan, R.Taneja, B.Mondragon, A.

(2010) Structure 18: 829-838

  • DOI: 10.1016/j.str.2010.03.006
  • Primary Citation of Related Structures:  3M6Z, 3M7D, 3M7G

  • PubMed Abstract: 
  • Topoisomerase V is an archaeal type I topoisomerase that is unique among topoisomerases due to presence of both topoisomerase and DNA repair activities in the same protein. It is organized as an N-terminal topoisomerase domain followed by 24 tandem h ...

    Topoisomerase V is an archaeal type I topoisomerase that is unique among topoisomerases due to presence of both topoisomerase and DNA repair activities in the same protein. It is organized as an N-terminal topoisomerase domain followed by 24 tandem helix-hairpin-helix (HhH) motifs. Structural studies have shown that the active site is buried by the (HhH) motifs. Here we show that the N-terminal domain can relax DNA in the absence of any HhH motifs and that the HhH motifs are required for stable protein-DNA complex formation. Crystal structures of various topoisomerase V fragments show changes in the relative orientation of the domains mediated by a long bent linker helix, and these movements are essential for the DNA to enter the active site. Phosphate ions bound to the protein near the active site helped model DNA in the topoisomerase domain and show how topoisomerase V may interact with DNA.


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Topoisomerase V
A, B
380Methanopyrus kandleriGene Names: top5
Find proteins for Q977W1 (Methanopyrus kandleri)
Go to UniProtKB:  Q977W1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.241 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.090α = 90.00
b = 70.090β = 90.00
c = 349.630γ = 90.00
Software Package:
Software NamePurpose
MD2-microdiffractometerdata collection
XDSdata reduction
SHARPphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance