Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 61.49 kDa 
• Atom Count: 4664 
• Modelled Residue Count: 538 
• Deposited Residue Count: 541 
• Unique protein chains: 1

3DJL

Crystal structure of alkylation response protein E. coli AidB

• DOI: 10.2210/pdb3DJL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-23 Released: 2008-09-23 
• Deposition Author(s): Eichman, B.F., Metz, A.H., Bowles, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.179 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 

Literature

Structure and DNA binding of alkylation response protein AidB.

Bowles, T., Metz, A.H., O'Quin, J., Wawrzak, Z., Eichman, B.F.

(2008) Proc Natl Acad Sci U S A 105: 15299-15304

• PubMed: 18829440 
• DOI: 10.1073/pnas.0806521105
• Primary Citation of Related Structures:  
  3DJL


• PubMed Abstract: 
  

Exposure of Escherichia coli to alkylating agents activates expression of AidB in addition to DNA repair proteins Ada, AlkA, and AlkB. AidB was recently shown to possess a flavin adenine dinucleotide (FAD) cofactor and to bind to dsDNA, implicating it as a flavin-dependent DNA repair enzyme. However, the molecular mechanism by which AidB acts to reduce the mutagenic effects of specific DNA alkylators is unknown. We present a 1.7-A crystal structure of AidB, which bears superficial resemblance to the acyl-CoA dehydrogenase superfamily of flavoproteins. The structure reveals a unique quaternary organization and a distinctive FAD active site that provides a rationale for AidB's limited dehydrogenase activity. A highly electropositive C-terminal domain not present in structural homologs was identified by mutational analysis as the DNA binding site. Structural analysis of the DNA and FAD binding sites provides evidence against AidB-catalyzed DNA repair and supports a model in which AidB acts to prevent alkylation damage by protecting DNA and destroying alkylating agents that have yet to reach their DNA target.

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Organizational Affiliation: 

Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein aidB	A	541	Escherichia coli	Mutation(s): 0  Gene Names: aidB EC: 1.3.99
UniProt
Find proteins for P33224 (Escherichia coli (strain K12)) Explore P33224  Go to UniProtKB:  P33224

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.179 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.989	α = 90
b = 101.875	β = 90
c = 137.566	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2008-06-23 
• Released Date: 2008-09-23 
Deposition Author(s): Eichman, B.F., Metz, A.H., Bowles, T.

Revision History  

• Version 1.0: 2008-09-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2012-03-21
  Changes: Database references, Derived calculations