2NMV

Damage detection by the UvrABC pathway: Crystal structure of UvrB bound to fluorescein-adducted DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Damage detection by the UvrABC pathway: crystal structure of UvrB bound to fluorescein-adducted DNA

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

(2006) FEBS Lett 580: 6423-6427

  • DOI: 10.1016/j.febslet.2006.10.051
  • Primary Citation of Related Structures:  
    2NMV

  • PubMed Abstract: 
  • UvrB is the damage recognition element of the highly conserved UvrABC pathway that functions in the removal of bulky DNA adducts. Pivotal to this is the formation of a damage detection complex that relies on the ability of UvrB to locate and sequester diverse lesions ...

    UvrB is the damage recognition element of the highly conserved UvrABC pathway that functions in the removal of bulky DNA adducts. Pivotal to this is the formation of a damage detection complex that relies on the ability of UvrB to locate and sequester diverse lesions. Whilst structures of UvrB bound to DNA have recently been reported, none address the issue of lesion recognition. Here, we describe the crystal structure of UvrB bound to a pentanucleotide containing a single fluorescein-adducted thymine that reveals a unique mechanism for damage detection entirely dependent on the exclusion of lesions larger than an undamaged nucleotide.


    Organizational Affiliation

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



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
UvrABC system protein BC [auth B]38Bacillus 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*TP*TP*T)-3'A [auth D]5N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP (Subject of Investigation/LOI)
    Query on ADP

    Download Ideal Coordinates CCD File 
    F [auth A]ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N
     Ligand Interaction
    FLU (Subject of Investigation/LOI)
    Query on FLU

    Download Ideal Coordinates CCD File 
    E [auth D]2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID
    C20 H12 O5
    YKGGGCXBWXHKIZ-UHFFFAOYSA-N
     Ligand Interaction
    NML
    Query on NML

    Download Ideal Coordinates CCD File 
    DN-METHYLACETAMIDE
    C3 H7 N O
    OHLUUHNLEMFGTQ-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.95 Å
    • R-Value Free: 0.281 
    • R-Value Work: 0.224 
    • R-Value Observed: 0.227 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 74.41α = 90
    b = 95.597β = 90
    c = 97.878γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    ADSCdata collection
    MOSFLMdata reduction
    CCP4data scaling
    MOLREPphasing

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2007-01-16
      Type: Initial release
    • Version 1.1: 2008-05-01
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance