2FDC

Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for DNA recognition and processing by UvrB.

Truglio, J.J.Karakas, E.Rhau, B.Wang, H.DellaVecchia, M.J.Van Houten, B.Kisker, C.

(2006) Nat Struct Mol Biol 13: 360-364

  • DOI: 10.1038/nsmb1072
  • Primary Citation of Related Structures:  
    2FDC

  • PubMed Abstract: 
  • DNA-damage recognition in the nucleotide excision repair (NER) cascade is a complex process, operating on a wide variety of damages. UvrB is the central component in prokaryotic NER, directly involved in DNA-damage recognition and guiding the DNA through repair synthesis ...

    DNA-damage recognition in the nucleotide excision repair (NER) cascade is a complex process, operating on a wide variety of damages. UvrB is the central component in prokaryotic NER, directly involved in DNA-damage recognition and guiding the DNA through repair synthesis. We report the first structure of a UvrB-double-stranded DNA complex, providing insights into the mechanism by which UvrB binds DNA, leading to formation of the preincision complex. One DNA strand, containing a 3' overhang, threads behind a beta-hairpin motif of UvrB, indicating that this motif inserts between the strands of the double helix, thereby locking down either the damaged or undamaged strand. The nucleotide directly behind the beta-hairpin is flipped out and inserted into a small, highly conserved pocket in UvrB.


    Organizational Affiliation

    Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-5115, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UvrABC system protein B AB658[Bacillus] caldotenaxMutation(s): 0 
Gene Names: uvrB
Find proteins for P56981 (Bacillus caldotenax)
Explore P56981 
Go to UniProtKB:  P56981
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(P*CP*GP*GP*CP*TP*CP*CP*AP*TP*CP*TP*CP*TP*AP*CP*CP*GP*CP*AP*A)-3'C, D20N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    FLQ
    Query on FLQ

    Download Ideal Coordinates CCD File 
    C
    N-[6-(ACETYLAMINO)HEXYL]-3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-6-CARBOXAMIDE
    C29 H28 N2 O7
    NYDPRVGMTFCAQC-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.30 Å
    • R-Value Free: 0.258 
    • R-Value Work: 0.205 
    • R-Value Observed: 0.210 
    • Space Group: P 32 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 153.265α = 90
    b = 153.265β = 90
    c = 160.17γ = 120
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    REFMACrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data reduction
    AMoREphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2006-03-14
      Type: Initial release
    • Version 1.1: 2008-05-01
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Advisory, Version format compliance
    • Version 1.3: 2017-10-18
      Changes: Refinement description