Web Release Date: February 24,
Structure of the Redox Sensor Domain of Azotobacter vinelandii NifL at Atomic
Resolution: Signaling, Dimerization, and Mechanism
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Department of Biochemistry and Molecular Biology, Consortium for Advanced Radiation Sources, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, and Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
Received September 30, 2006
Revised Manuscript Received January 23, 2007
Abstract:
NifL is a multidomain sensor protein responsible for the transcriptional regulation of genes
involved in response to changes in cellular redox state and ADP concentration. Cellular redox is monitored
by the N-terminal PAS domain of NifL which contains an FAD cofactor. Flavin-based PAS domains of
this type have also been referred to as LOV domains. To explore the mechanism of signal recognition
and transduction in NifL, we determined the crystal structure of the FAD-bound PAS domain of NifL
from Azotobacter vinelandii to 1.04 Å resolution. The structure reveals a novel cavity within the PAS
domain which contains two water molecules directly coordinated to the FAD. This cavity is connected to
solvent by multiple access channels which may facilitate the oxidation of the FAD by molecular oxygen
and the release of hydrogen peroxide. The structure contains a dimer of the NifL PAS domain that is
structurally very similar to those described in other crystal structures of PAS domains and identifies a
conserved dimerization motif. An N-terminal amphipathic helix constitutes part of the dimerization interface,
and similar N-terminal helices are identified in other PAS domain proteins. The structure suggests a model
for redox-mediated signaling in which a conformational change is initiated by redox-dependent changes
in protonation at the N5 atom of FAD that lead to reorganization of hydrogen bonds within the flavin
binding pocket. A structural signal is subsequently transmitted to the 
-sheet interface between the
monomers of the PAS domain.
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