1CY1

COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'PTPTPT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Protein-nucleotide interactions in E. coli DNA topoisomerase I.

Feinberg, H.Changela, A.Mondragon, A.

(1999) Nat Struct Biol 6: 961-968

  • DOI: https://doi.org/10.1038/13333
  • Primary Citation of Related Structures:  
    1CY0, 1CY1, 1CY2, 1CY4, 1CY6, 1CY7, 1CY8

  • PubMed Abstract: 

    DNA topoisomerases are the enzymes responsible for controlling and maintaining the topological states of DNA. Type IA enzymes work by transiently breaking the phosphodiester backbone of one strand to allow passage of another strand through the break. The protein has to perform complex rearrangements of the DNA, and hence it is likely that different regions of the enzyme bind DNA with different affinities. In order to identify some of the DNA binding sites in the protein, we have solved the structures of several complexes of the 67 kDa N-terminal fragment of Escherichia coli DNA topoisomerase I with mono- and trinucleotides. There are five different binding sites in the complexes, one of which is adjacent to the active site. Two other sites are in the central hole of the protein and may represent general DNA binding regions. The positions of these sites allow us to identify different DNA binding regions and to understand their possible roles in the catalytic cycle.


  • Organizational Affiliation

    Department of Biochemistry, Molecular Biology and Cell Biology, Northwerstern University, 2153 Sheridan Road, Evanston, Illinois 60208, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA TOPOISOMERASE I599Escherichia coli K-12Mutation(s): 0 
EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
UniProt
Find proteins for P06612 (Escherichia coli (strain K12))
Explore P06612 
Go to UniProtKB:  P06612
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06612
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.86α = 90
b = 77.8β = 90
c = 138.66γ = 90
Software Package:
Software NamePurpose
CNSrefinement
REFMACrefinement
X-PLORrefinement
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection
  • Version 1.5: 2022-12-21
    Changes: Database references, Derived calculations
  • Version 1.6: 2024-05-22
    Changes: Data collection