1K4S

HUMAN DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The mechanism of topoisomerase I poisoning by a camptothecin analog

Staker, B.L.Hjerrild, K.Feese, M.D.Behnke, C.A.Burgin Jr., A.B.Stewart, L.J.

(2002) Proc.Natl.Acad.Sci.USA 99: 15387-15392

  • DOI: 10.1073/pnas.242259599
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the x-ray crystal structure of human topoisomerase I covalently joined to double-stranded DNA and bound to the clinically approved anticancer agent Topotecan. Topotecan mimics a DNA base pair and binds at the site of DNA cleavage by interca ...

    We report the x-ray crystal structure of human topoisomerase I covalently joined to double-stranded DNA and bound to the clinically approved anticancer agent Topotecan. Topotecan mimics a DNA base pair and binds at the site of DNA cleavage by intercalating between the upstream (-1) and downstream (+1) base pairs. Intercalation displaces the downstream DNA, thus preventing religation of the cleaved strand. By specifically binding to the enzyme-substrate complex, Topotecan acts as an uncompetitive inhibitor. The structure can explain several of the known structure-activity relationships of the camptothecin family of anticancer drugs and suggests that there are at least two classes of mutations that can produce a drug-resistant enzyme. The first class includes changes to residues that contribute to direct interactions with the drug, whereas a second class would alter interactions with the DNA and thereby destabilize the drug-binding site.


    Organizational Affiliation

    deCODE genetics, Incorporated, BioStructures Group, 7869 Northeast Day Road West, Bainbridge Island, WA 98110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase I
A
592Homo sapiensMutation(s): 0 
Gene Names: TOP1
EC: 5.6.2.1
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*(5IU)P*(5IU))-3'B10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*(SPT)P*GP*AP*AP*AP*AP*AP*(5IU)P*(5IU)P*(5IU)P*(5IU)P*T)-3'C12N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*AP*AP*AP*AP*AP*TP*(IDO)UP*(IDO)UP*(IDO)UP*(IDO)UP*CP*AP*AP*AP*GP*(IDO)UP*CP*(IDO)UP*(IDO)UP*(IDO)UP*(IDO)UP*T)-3'D22N/A
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
SPT
Query on SPT
C
DNA LINKINGC10 H15 N2 O7 P SDT
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
5IU
Query on 5IU
B, C, D
DNA LINKINGC9 H12 I N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.217 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 73.235α = 90.00
b = 73.235β = 90.00
c = 186.632γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNXrefinement
DENZOdata reduction
CNXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance