1D9Z

CRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB IN COMPLEX WITH ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of UvrB, a DNA helicase adapted for nucleotide excision repair.

Theis, K.Chen, P.J.Skorvaga, M.Van Houten, B.Kisker, C.

(1999) EMBO J. 18: 6899-6907

  • DOI: 10.1093/emboj/18.24.6899
  • Primary Citation of Related Structures:  1D9X

  • PubMed Abstract: 
  • Nucleotide excision repair (NER) is a highly conserved DNA repair mechanism. NER systems recognize the damaged DNA strand, cleave it on both sides of the lesion, remove and newly synthesize the fragment. UvrB is a central component of the bacterial N ...

    Nucleotide excision repair (NER) is a highly conserved DNA repair mechanism. NER systems recognize the damaged DNA strand, cleave it on both sides of the lesion, remove and newly synthesize the fragment. UvrB is a central component of the bacterial NER system participating in damage recognition, strand excision and repair synthesis. We have solved the crystal structure of UvrB in the apo and the ATP-bound forms. UvrB contains two domains related in structure to helicases, and two additional domains unique to repair proteins. The structure contains all elements of an intact helicase, and is evidence that UvrB utilizes ATP hydrolysis to move along the DNA to probe for damage. The location of conserved residues and structural comparisons allow us to predict the path of the DNA and suggest that the tight pre-incision complex of UvrB and the damaged DNA is formed by insertion of a flexible beta-hairpin between the two DNA strands.


    Related Citations: 
    • Strand opening by the UvrA2B complex allows dynamic recognition of DNA damage
      Zou, Y.,Van Houten, B.
      (1999) Embo J. 18: 4889


    Organizational Affiliation

    Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794-8651, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXCINUCLEASE UVRABC COMPONENT UVRB
A
657Bacillus caldotenaxGene Names: uvrB
Find proteins for P56981 (Bacillus caldotenax)
Go to UniProtKB:  P56981
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.262 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 153.443α = 90.00
b = 153.443β = 90.00
c = 80.741γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
MAR345data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description