1A36

TOPOISOMERASE I/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

A model for the mechanism of human topoisomerase I.

Stewart, L.Redinbo, M.R.Qiu, X.Hol, W.G.Champoux, J.J.

(1998) Science 279: 1534-1541

  • DOI: https://doi.org/10.1126/science.279.5356.1534
  • Primary Citation of Related Structures:  
    1A36

  • PubMed Abstract: 

    The three-dimensional structure of a 70-kilodalton amino terminally truncated form of human topoisomerase I in complex with a 22-base pair duplex oligonucleotide, determined to a resolution of 2.8 angstroms, reveals all of the structural elements of the enzyme that contact DNA. The linker region that connects the central core of the enzyme to the carboxyl-terminal domain assumes a coiled-coil configuration and protrudes away from the remainder of the enzyme. The positively charged DNA-proximal surface of the linker makes only a few contacts with the DNA downstream of the cleavage site. In combination with the crystal structures of the reconstituted human topoisomerase I before and after DNA cleavage, this information suggests which amino acid residues are involved in catalyzing phosphodiester bond breakage and religation. The structures also lead to the proposal that the topoisomerization step occurs by a mechanism termed "controlled rotation."


  • Organizational Affiliation

    Biomolecular Structure Center and Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA 98195-7742, USA. emerald_biostructures@rocketmail.com


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TOPOISOMERASE IC [auth A]591Homo sapiensMutation(s): 1 
EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11387 (Homo sapiens)
Explore P11387 
Go to UniProtKB:  P11387
PHAROS:  P11387
GTEx:  ENSG00000198900 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11387
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*AP*GP*AP*AP*AP*AP*A P*TP*TP*TP*TP*T)- 3')A [auth B]22N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*AP*AP*GP*TP*C P*TP*TP*TP*TP*T)- 3')B [auth C]22N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.5α = 90
b = 118.4β = 101.2
c = 71.5γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-08-12
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references
  • Version 1.4: 2024-02-07
    Changes: Data collection
  • Version 1.5: 2024-04-03
    Changes: Refinement description