3V4R | pdb_00003v4r

Crystal structure of a UvrB dimer-DNA complex

• PDB DOI: https://doi.org/10.2210/pdb3V4R/pdb
• NAKB: 3V4R

• Classification: HYDROLASE/DNA
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-12-15 Released: 2012-07-04 
• Deposition Author(s): Webster, M.P.J., Jukes, R., Barrett, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 
  0.219 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the UvrB dimer: insights into the nature and functioning of the UvrAB damage engagement and UvrB-DNA complexes.

Webster, M.P., Jukes, R., Zamfir, V.S., Kay, C.W., Bagneris, C., Barrett, T.

(2012) Nucleic Acids Res 40: 8743-8758

• PubMed: 22753105 
• DOI: https://doi.org/10.1093/nar/gks633
• Primary Citation Related Structures: 
  3V4R


• PubMed Abstract: 
  

  UvrB has a central role in the highly conserved UvrABC pathway functioning not only as a damage recognition element but also as an essential component of the lesion tracking machinery. While it has been recently confirmed that the tracking assembly comprises a UvrA2B2 heterotetramer, the configurations of the damage engagement and UvrB-DNA handover complexes remain obscure. Here, we present the first crystal structure of a UvrB dimer whose biological significance has been verified using both chemical cross-linking and electron paramagnetic resonance spectroscopy. We demonstrate that this dimeric species stably associates with UvrA and forms a UvrA2B2-DNA complex. Our studies also illustrate how signals are transduced between the ATP and DNA binding sites to generate the helicase activity pivotal to handover and formation of the UvrB2-DNA complex, providing key insights into the configurations of these important repair intermediates.

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Organizational Affiliation: 
• Department of Biological Sciences, Institute of Structural and Molecular Biology, Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 160.21 kDa 
• Atom Count: 8,815 
• Modeled Residue Count: 1,179 
• Deposited Residue Count: 1,350 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UvrABC system protein B	A, B	667	Bacillus subtilis	Mutation(s): 0  Gene Names: BSU35170, dinA, uvr, uvrB EC: 3.1.21.5
UniProt
Find proteins for P37954 (Bacillus subtilis (strain 168)) Explore P37954  Go to UniProtKB:  P37954

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA: 5 -TACTGTTT-3	C, D	8	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free:  0.219 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.94	α = 90
b = 100.31	β = 90
c = 163.63	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-04 
Deposition Author(s): Webster, M.P.J., Jukes, R., Barrett, T.

Revision History  

• Version 1.0: 2012-07-04
  Type: Initial release
  
• Version 1.1: 2012-10-10
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description