2FDC | pdb_00002fdc

Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex

• PDB DOI: https://doi.org/10.2210/pdb2FDC/pdb
• NAKB: 2FDC

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


• Deposited: 2005-12-13 Released: 2006-03-14 
• Deposition Author(s): Truglio, J.J., Kisker, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.258 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Structural basis for DNA recognition and processing by UvrB.

Truglio, J.J., Karakas, E., Rhau, B., Wang, H., DellaVecchia, M.J., Van Houten, B., Kisker, C.

(2006) Nat Struct Mol Biol 13: 360-364

• PubMed: 16532007 
• DOI: https://doi.org/10.1038/nsmb1072
• Primary Citation Related Structures: 
  2FDC


• PubMed Abstract: 
  

  DNA-damage recognition in the nucleotide excision repair (NER) cascade is a complex process, operating on a wide variety of damages. UvrB is the central component in prokaryotic NER, directly involved in DNA-damage recognition and guiding the DNA through repair synthesis. We report the first structure of a UvrB-double-stranded DNA complex, providing insights into the mechanism by which UvrB binds DNA, leading to formation of the preincision complex. One DNA strand, containing a 3' overhang, threads behind a beta-hairpin motif of UvrB, indicating that this motif inserts between the strands of the double helix, thereby locking down either the damaged or undamaged strand. The nucleotide directly behind the beta-hairpin is flipped out and inserted into a small, highly conserved pocket in UvrB.

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Organizational Affiliation: 
• Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-5115, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 163.72 kDa 
• Atom Count: 9,178 
• Modeled Residue Count: 1,107 
• Deposited Residue Count: 1,356 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UvrABC system protein B	C [auth A], D [auth B]	658	[Bacillus] caldotenax	Mutation(s): 0  Gene Names: uvrB
UniProt
Find proteins for P56981 (Bacillus caldotenax) Explore P56981  Go to UniProtKB:  P56981

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(P*CP*GP*GP*CP*TP*CP*CP*AP*TP*CP*TP*CP*TP*AP*CP*CP*GP*CP*AP*A)-3'	A [auth C], B [auth D]	20	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLQ	E [auth C]	N-[6-(ACETYLAMINO)HEXYL]-3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-6-CARBOXAMIDE C29 H28 N2 O7 NYDPRVGMTFCAQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.258 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.265	α = 90
b = 153.265	β = 90
c = 160.17	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-14 
Deposition Author(s): Truglio, J.J., Kisker, C.

Revision History  

• Version 1.0: 2006-03-14
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations