6O8H | pdb_00006o8h

Crystal structure of UvrB mutant bound to duplex DNA

• PDB DOI: https://doi.org/10.2210/pdb6O8H/pdb
• NAKB: 6O8H

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): [Bacillus] caldotenax, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-10 Released: 2020-01-22 
• Deposition Author(s): Lee, S.-J., Verdine, G.L.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.277 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Mechanism of DNA Lesion Homing and Recognition by the Uvr Nucleotide Excision Repair System.

Lee, S.J., Sung, R.J., Verdine, G.L.

(2019) Research (Wash D C) 2019: 5641746-5641746

• PubMed: 31549070 
• DOI: https://doi.org/10.34133/2019/5641746
• Primary Citation Related Structures: 
  6O8E, 6O8F, 6O8G, 6O8H


• PubMed Abstract: 
  

  Nucleotide excision repair (NER) is an essential DNA repair system distinguished from other such systems by its extraordinary versatility. NER removes a wide variety of structurally dissimilar lesions having only their bulkiness in common. NER can also repair several less bulky nucleobase lesions, such as 8-oxoguanine. Thus, how a single DNA repair system distinguishes such a diverse array of structurally divergent lesions from undamaged DNA has been one of the great unsolved mysteries in the field of genome maintenance. Here we employ a synthetic crystallography approach to obtain crystal structures of the pivotal NER enzyme UvrB in complex with duplex DNA, trapped at the stage of lesion-recognition. These structures coupled with biochemical studies suggest that UvrB integrates the ATPase-dependent helicase/translocase and lesion-recognition activities. Our work also conclusively establishes the identity of the lesion-containing strand and provides a compelling insight to how UvrB recognizes a diverse array of DNA lesions.

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Organizational Affiliation: 
• Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 78.14 kDa 
• Atom Count: 5,323 
• Modeled Residue Count: 597 
• Deposited Residue Count: 625 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UvrABC system protein B	A	593	[Bacillus] caldotenax	Mutation(s): 0  Gene Names: uvrB
UniProt
Find proteins for P56981 (Bacillus caldotenax) Explore P56981  Go to UniProtKB:  P56981

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*AP*TP*CP*GP*CP*GP*CP*TP*AP*CP*C)-3')	B	16	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*CP*GP*CP*GP*AP*TP*GP*GP*AP*GP*A)-3')	C	16	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.277 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.791	α = 90
b = 124.791	β = 90
c = 96.175	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-01-22 
Deposition Author(s): Lee, S.-J., Verdine, G.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2020-01-22
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Advisory, Data collection, Database references