2D7D

Structural insights into the cryptic DNA dependent ATP-ase activity of UvrB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into the cryptic DNA-dependent ATPase activity of UvrB

Eryilmaz, J.Ceschini, S.Ryan, J.Geddes, S.Waters, T.R.Barrett, T.E.

(2006) J.Mol.Biol. 357: 62-72

  • DOI: 10.1016/j.jmb.2005.12.059

  • PubMed Abstract: 
  • The UvrABC pathway is a ubiquitously occurring mechanism targeted towards the repair of bulky base damage. Key to this process is UvrB, a DNA-dependent limited helicase that acts as a lesion recognition element whilst part of a tracking complex invol ...

    The UvrABC pathway is a ubiquitously occurring mechanism targeted towards the repair of bulky base damage. Key to this process is UvrB, a DNA-dependent limited helicase that acts as a lesion recognition element whilst part of a tracking complex involving UvrA, and as a DNA-binding platform required for the presentation of damage to UvrC for subsequent processing. We have been able to determine the structure of a ternary complex involving UvrB* (a C-terminal truncation of full-length UvrB), a polythymine trinucleotide and ADP. This structure has highlighted the roles of key conserved residues in DNA binding distinct from those of the beta-hairpin, where most of the attention in previous studies has been focussed. We are also the first to report the structural basis underlying conformational re-modelling of the beta-hairpin that is absolutely required for DNA binding and how this event results in an ATPase primed for catalysis. Our data provide the first insights at the molecular level into the transformation of UvrB into an active helicase.


    Related Citations: 
    • Structural insights into the cryptic ATP-ase activity of UvrB
      Eryilmaz, J.,Ceschini, S.,Ryan, J.,Geddes, S.,Waters, T.R.,Barrett, T.E.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    The School of Crystallography and the Institute for Structural Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UvrABC system protein B
A
661Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: uvrB (dinA, uvr)
Find proteins for P37954 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P37954
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40-mer from UvrABC system protein B
B
40Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: uvrB (dinA, uvr)
Find proteins for P37954 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P37954
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(P*TP*TP*T)-3'D3N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.231α = 90.00
b = 98.215β = 90.00
c = 95.405γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MOSFLMdata reduction
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-11-18 
  • Released Date: 2006-05-02 
  • Deposition Author(s): Barrett, T.E.

Revision History 

  • Version 1.0: 2006-05-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance