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: 3.3 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.205 

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

  • 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 thr ...

    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: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UvrABC system protein B
A, B
658Bacillus caldotenaxGene Names: uvrB
Find proteins for P56981 (Bacillus caldotenax)
Go to UniProtKB:  P56981
Entity ID: 1
MoleculeChainsLengthOrganism
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 SDF File 
Download CCD File 
C
N-[6-(ACETYLAMINO)HEXYL]-3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-6-CARBOXAMIDE
FLUORESCEIN ADDUCT
C29 H28 N2 O7
NYDPRVGMTFCAQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.205 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 153.265α = 90.00
b = 153.265β = 90.00
c = 160.170γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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