3UWX

Crystal structure of UvrA-UvrB complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.398 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.288 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and mechanism of the UvrA-UvrB DNA damage sensor.

Pakotiprapha, D.Samuels, M.Shen, K.Hu, J.H.Jeruzalmi, D.

(2012) Nat.Struct.Mol.Biol. 19: 291-298

  • DOI: 10.1038/nsmb.2240
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nucleotide excision repair (NER) is used by all organisms to eliminate DNA lesions. We determined the structure of the Geobacillus stearothermophilus UvrA-UvrB complex, the damage-sensor in bacterial NER and a new structure of UvrA. We observe that t ...

    Nucleotide excision repair (NER) is used by all organisms to eliminate DNA lesions. We determined the structure of the Geobacillus stearothermophilus UvrA-UvrB complex, the damage-sensor in bacterial NER and a new structure of UvrA. We observe that the DNA binding surface of UvrA, previously found in an open shape that binds damaged DNA, also exists in a closed groove shape compatible with native DNA only. The sensor contains two UvrB molecules that flank the UvrA dimer along the predicted path for DNA, ~80 Å from the lesion. We show that the conserved signature domain II of UvrA mediates a nexus of contacts among UvrA, UvrB and DNA. Further, in our new structure of UvrA, this domain adopts an altered conformation while an adjacent nucleotide binding site is vacant. Our findings raise unanticipated questions about NER and also suggest a revised picture of its early stages.


    Organizational Affiliation

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Excinuclease ABC, A subunit
A
972Geobacillus sp. (strain Y412MC52)Mutation(s): 0 
Gene Names: uvrA
Find proteins for A0A0E0TG05 (Geobacillus sp. (strain Y412MC52))
Go to UniProtKB:  A0A0E0TG05
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UvrABC system protein B
B
683Geobacillus sp. (strain Y412MC52)Mutation(s): 0 
Gene Names: uvrB
Find proteins for A0A0E0TGM2 (Geobacillus sp. (strain Y412MC52))
Go to UniProtKB:  A0A0E0TGM2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.398 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.288 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 216.823α = 90.00
b = 216.823β = 90.00
c = 116.802γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-03-21
    Type: Database references