2D7D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 

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
  • Primary Citation of Related Structures:  
    2D7D

  • 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 involving UvrA, and as a DNA-binding platform required for the presentation of damage to UvrC for subsequent processing ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UvrABC system protein BB [auth A]661Bacillus subtilisMutation(s): 0 
Gene Names: uvrB
EC: 3.1
UniProt
Find proteins for P37954 (Bacillus subtilis (strain 168))
Explore P37954 
Go to UniProtKB:  P37954
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40-mer from UvrABC system protein BC [auth B]40Bacillus subtilisMutation(s): 0 
Gene Names: uvrB
EC: 3.1
UniProt
Find proteins for P37954 (Bacillus subtilis (strain 168))
Explore P37954 
Go to UniProtKB:  P37954
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(P*TP*TP*T)-3'A [auth D]3N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP
    Query on ADP

    Download Ideal Coordinates CCD File 
    D [auth A]ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.10 Å
    • R-Value Free: 0.285 
    • R-Value Work: 0.227 
    • R-Value Observed: 0.230 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 74.231α = 90
    b = 98.215β = 90
    c = 95.405γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    MOSFLMdata reduction
    CCP4data scaling
    MOLREPphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

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

    Revision History  (Full details and data files)

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