1LPQ

Human DNA Topoisomerase I (70 Kda) In Non-Covalent Complex With A 22 Base Pair DNA Duplex Containing an 8-oxoG Lesion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

8-Oxoguanine rearranges the active site of human topoisomerase I

Lesher, D.T.Pommier, Y.Stewart, L.Redinbo, M.R.

(2002) Proc.Natl.Acad.Sci.USA 99: 12102-12107

  • DOI: 10.1073/pnas.192282699

  • PubMed Abstract: 
  • 7,8-Dihydro-8-oxoguanine (8-oxoG) is the most common form of oxidative DNA damage in human cells. Biochemical studies have shown that 8-oxoG decreases the DNA cleavage activity of human topoisomerase I, an enzyme vital to DNA metabolism and stability ...

    7,8-Dihydro-8-oxoguanine (8-oxoG) is the most common form of oxidative DNA damage in human cells. Biochemical studies have shown that 8-oxoG decreases the DNA cleavage activity of human topoisomerase I, an enzyme vital to DNA metabolism and stability. We present the 3.1-A crystal structure of human topoisomerase I in noncovalent complex with a DNA oligonucleotide containing 8-oxoG at the +1 position in the scissile strand. We find that 8-oxoG reorganizes the active site of human topoisomerase I into an inactive conformation relative to the structures of topoisomerase I-DNA complexes elucidated previously. The catalytic Tyr-723-Phe rotates away from the DNA cleavage site and packs into the body of the molecule. A second active-site residue, Arg-590, becomes disordered and is not observed in the structure. The docked, inactive conformation of Tyr-723-Phe is reminiscent of the related tyrosine recombinase family of integrases and recombinases, suggesting a common regulatory mechanism. We propose that human topoisomerase I binds to DNA first in an inactive conformation and then rearranges its active site for catalysis. 8-OxoG appears to impact topoisomerase I by stabilizing the inactive, DNA-bound state.


    Organizational Affiliation

    Departments of Chemistry and Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase I
A
564Homo sapiensGene Names: TOP1
EC: 5.99.1.2
Find proteins for P11387 (Homo sapiens)
Go to Gene View: TOP1
Go to UniProtKB:  P11387
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*(8OG)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'B22N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'C22N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
8OG
Query on 8OG
B
DNA LINKINGC10 H14 N5 O8 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.256 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.200α = 90.00
b = 122.500β = 97.40
c = 72.000γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-16
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance