1NH3

Human Topoisomerase I Ara-C Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Impact of the Leukemia Drug 1-beta-D-Arabinofuranosylcytosine (Ara-C) on the Covalent Human Topoisomerase I-DNA Complex

Chrencik, J.E.Burgin, A.B.Pommier, Y.Stewart, L.Redinbo, M.R.

(2003) J Biol Chem 278: 12461-12466

  • DOI: 10.1074/jbc.M212930200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 1-beta-d-Arabinofuranosylcytosine (Ara-C) is a potent antineoplastic drug used in the treatment of acute leukemia. Previous biochemical studies indicated the incorporation of Ara-C into DNA reduced the catalytic activity of human topoisomerase I by d ...

    1-beta-d-Arabinofuranosylcytosine (Ara-C) is a potent antineoplastic drug used in the treatment of acute leukemia. Previous biochemical studies indicated the incorporation of Ara-C into DNA reduced the catalytic activity of human topoisomerase I by decreasing the rate of single DNA strand religation by the enzyme by 2-3-fold. We present the 3.1 A crystal structure of human topoisomerase I in covalent complex with an oligonucleotide containing Ara-C at the +1 position of the non-scissile DNA strand. The structure reveals that a hydrogen bond formed between the 2'-hydroxyl of Ara-C and the O4' of the adjacent -1 base 5' to the damage site stabilizes a C3'-endo pucker in the Ara-C arabinose ring. The structural distortions at the site of damage are translated across the DNA double helix to the active site of human topoisomerase I. The free sulfhydryl at the 5'-end of the nicked DNA strand in this trapped covalent complex is shifted out of alignment with the 3'-phosphotyrosine linkage at the catalytic tyrosine 723 residue, producing a geometry not optimal for religation. The subtle structural changes caused by the presence of Ara-C in the DNA duplex may contribute to the cytotoxicity of this leukemia drug by prolonging the lifetime of the covalent human topoisomerase I-DNA complex.


    Organizational Affiliation

    Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase IA563Homo sapiensMutation(s): 1 
Gene Names: TOP1
EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
Find proteins for P11387 (Homo sapiens)
Explore P11387 
Go to UniProtKB:  P11387
NIH Common Fund Data Resources
PHAROS  P11387
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*UP*(UBB))-3'B10N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*(GNG)P*GP*AP*AP*AP*AP*AP*UP*UP*UP*UP*T)-3'C12N/A

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Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*AP*AP*AP*AP*AP*TP*UP*UP*UP*UP*CP*(CAR)P*AP*AP*GP*UP*CP*UP*UP*UP*UP*T)-3'D22N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
AL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.97α = 90
b = 72.97β = 90
c = 186.29γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance