3DJL

Crystal structure of alkylation response protein E. coli AidB

Summary for 3DJL

• Entry DOI: 10.2210/pdb3djl/pdb
• Descriptor: Protein aidB, CALCIUM ION, FLAVIN-ADENINE DINUCLEOTIDE, ... (4 entities in total)
• Functional Keywords: alpha helix, beta-barrel, fad, flavoprotein, oxidoreductase
• Biological source: Escherichia coli
• Cellular location: Cytoplasm (Potential): P33224
• Total number of polymer chains: 1
• Total formula weight: 61488.45

Authors

Eichman, B.F.,Metz, A.H.,Bowles, T. (deposition date: 2008-06-23, release date: 2008-09-23, Last modification date: 2024-11-13)

Primary citation

Bowles, T.,Metz, A.H.,O'Quin, J.,Wawrzak, Z.,Eichman, B.F.
Structure and DNA binding of alkylation response protein AidB.
Proc.Natl.Acad.Sci.USA, 105:15299-15304, 2008

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.

PubMed: 18829440
DOI: 10.1073/pnas.0806521105

Experimental method

X-RAY DIFFRACTION (1.7 Å)