2NMV | pdb_00002nmv

Damage detection by the UvrABC pathway: Crystal structure of UvrB bound to fluorescein-adducted DNA

• PDB DOI: https://doi.org/10.2210/pdb2NMV/pdb
• NAKB: 2NMV

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


• Deposited: 2006-10-23 Released: 2007-01-16 
• Deposition Author(s): Waters, T.R., Eryilmaz, J., Geddes, S., Barrett, T.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.281 (Depositor) 
• R-Value Work: 
  0.224 (Depositor) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Damage detection by the UvrABC pathway: crystal structure of UvrB bound to fluorescein-adducted DNA

Waters, T.R., Eryilmaz, J., Geddes, S., Barrett, T.E.

(2006) FEBS Lett 580: 6423-6427

• PubMed: 17097086 
• DOI: https://doi.org/10.1016/j.febslet.2006.10.051


• PubMed Abstract: 
  

  UvrB is the damage recognition element of the highly conserved UvrABC pathway that functions in the removal of bulky DNA adducts. Pivotal to this is the formation of a damage detection complex that relies on the ability of UvrB to locate and sequester diverse lesions. Whilst structures of UvrB bound to DNA have recently been reported, none address the issue of lesion recognition. Here, we describe the crystal structure of UvrB bound to a pentanucleotide containing a single fluorescein-adducted thymine that reveals a unique mechanism for damage detection entirely dependent on the exclusion of lesions larger than an undamaged nucleotide.

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Organizational Affiliation: 
• The School of Crystallography and the Institute for Structural Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 83.25 kDa 
• Atom Count: 5,311 
• Modeled Residue Count: 663 
• Deposited Residue Count: 704 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UvrABC system protein B	B [auth A]	661	Bacillus subtilis	Mutation(s): 0  Gene Names: uvrB EC: 3.1
UniProt
Find proteins for P37954 (Bacillus subtilis (strain 168)) Explore P37954  Go to UniProtKB:  P37954

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
UvrABC system protein B	C [auth B]	38	Bacillus subtilis	Mutation(s): 0  Gene Names: uvrB EC: 3.1
UniProt
Find proteins for P37954 (Bacillus subtilis (strain 168)) Explore P37954  Go to UniProtKB:  P37954

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(P*TP*TP*TP*TP*T)-3'	A [auth D]	5	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	F [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
FLU	E [auth D]	2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID C20 H12 O5 YKGGGCXBWXHKIZ-UHFFFAOYSA-N
NML	D	N-METHYLACETAMIDE C3 H7 N O OHLUUHNLEMFGTQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.281 (Depositor) 
• R-Value Work:  0.224 (Depositor) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.41	α = 90
b = 95.597	β = 90
c = 97.878	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-16 
Deposition Author(s): Waters, T.R., Eryilmaz, J., Geddes, S., Barrett, T.E.

Revision History  

• Version 1.0: 2007-01-16
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description