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 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/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. 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)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37954
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37954
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(P*TP*TP*TP*TP*T)-3'A [auth D]5N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
F [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
FLU
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
NML
Query on NML

Download Ideal Coordinates CCD File 
D
N-METHYLACETAMIDE
C3 H7 N O
OHLUUHNLEMFGTQ-UHFFFAOYSA-N
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

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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
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description