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 

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

  • 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 sequeste ...

    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: 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
UvrABC system protein B
B
38Bacillus 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*TP*TP*T)-3'D5N/A
Small Molecules
Ligands 3 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
NML
Query on NML

Download SDF File 
Download CCD File 
D
N-METHYLACETAMIDE
C3 H7 N O
OHLUUHNLEMFGTQ-UHFFFAOYSA-N
 Ligand Interaction
FLU
Query on FLU

Download SDF File 
Download CCD File 
D
2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID
FLUORESCEIN
C20 H12 O5
YKGGGCXBWXHKIZ-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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.410α = 90.00
b = 95.597β = 90.00
c = 97.878γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
REFMACrefinement
MOSFLMdata reduction
MOLREPphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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