Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 74.21 kDa 
• Atom Count: 4566 
• Modelled Residue Count: 564 
• Deposited Residue Count: 670 
• Unique protein chains: 1

3UX8

Crystal structure of UvrA

• DOI: 10.2210/pdb3UX8/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Geobacillus sp. Y412MC52
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-12-04 Released: 2012-02-08 
• Deposition Author(s): Samuels, M.A., Pakotiprapha, D., Jeruzalmi, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.245 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

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

• PubMed: 22307053 
• DOI: 10.1038/nsmb.2240
• Primary Citation of Related Structures:  
  3UX8, 3UWX


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Excinuclease ABC, A subunit	A	670	Geobacillus sp. Y412MC52	Mutation(s): 0  Gene Names: GYMC52_3203, uvrA
Find proteins for A0A0E0TG05 (Geobacillus sp. (strain Y412MC52)) Explore A0A0E0TG05  Go to UniProtKB:  A0A0E0TG05

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.245 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.653	α = 90
b = 51.33	β = 97.27
c = 112.395	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-12-04 
• Released Date: 2012-02-08 
Deposition Author(s): Samuels, M.A., Pakotiprapha, D., Jeruzalmi, D.

Revision History  

• Version 1.0: 2012-02-08
  Type: Initial release
  
• Version 1.1: 2012-05-09
  Changes: Database references
• Version 1.2: 2014-05-07
  Changes: Other
• Version 1.3: 2017-08-16
  Changes: Refinement description, Source and taxonomy