Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 75.63 kDa 
• Atom Count: 4717 
• Modelled Residue Count: 590 
• Deposited Residue Count: 658 
• Unique protein chains: 1

1D9X

CRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB

• PDB DOI: 10.2210/pdb1D9X/pdb

• Classification: GENE REGULATION
• Organism(s): [Bacillus] caldotenax
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-10-30 Released: 2000-05-03 
• Deposition Author(s): Theis, K., Chen, P.J., Skorvaga, M., Van Houten, B., Kisker, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.324 
• R-Value Work: 0.256 

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

• PubMed: 10601012 
• DOI: 10.1093/emboj/18.24.6899
• Primary Citation of Related Structures:  
  1D9X, 1D9Z


• 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 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.

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Related Citations: 

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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXCINUCLEASE UVRABC COMPONENT UVRB	A	658	[Bacillus] caldotenax	Mutation(s): 0  Gene Names: uvrB
UniProt
Find proteins for P56981 (Bacillus caldotenax) Explore P56981  Go to UniProtKB:  P56981

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.324 
• R-Value Work: 0.256 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.207	α = 90
b = 150.207	β = 90
c = 79.516	γ = 120

Software Package:

Software Name	Purpose
SHARP	phasing
REFMAC	refinement
X-PLOR	refinement
MARMAD	data reduction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-10-30 
• Released Date: 2000-05-03 
Deposition Author(s): Theis, K., Chen, P.J., Skorvaga, M., Van Houten, B., Kisker, C.

Revision History  

• Version 1.0: 2000-05-03
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2016-12-14
  Changes: Other