Structure of the Redox Sensor Domain of Azotobacter vinelandii NifL at Atomic Resolution:  Signaling, Dimerization, and Mechanism^,

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 A 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 beta-sheet interface between the monomers of the PAS domain.

Charting the Signal Trajectory in a Light-Oxygen-Voltage Photoreceptor by Random Mutagenesis and Covariance Analysis

“…6B) that forms the interface to the coaxial AЈ␣ and J␣ coiled-coils. Both the AЈ␣ and J␣ regions Nand C-terminal to the PAS domain core display helical signatures with numerous short-range sequential covarying pairs, in agreement with previous evidence for helical confirmation at both the sequence and structural levels (4,11,17,34). As our structural and functional data implicate the AЈ␣ and J␣ coiledcoils in signal transduction and modulation (see above and Ref.…”

Light-activated DNA binding in a designed allosteric protein

“…1B). LOV domains, widely distributed in modular signaling architectures, contain a cofactor-binding PAS domain flanked by aminoand/or carboxyl-terminal helices (23)(24)(25)(26). In AsLOV2, absorption of a photon leads to the formation of a covalent adduct between the flavin mononucleotide (FMN) cofactor and a conserved cysteine residue (27).…”

Role of the Cytoplasmic N-terminal Cap and Per-Arnt-Sim (PAS) Domain in Trafficking and Stabilization of Kv11.1 Channels

“…1A). In Kv11.1a channels, the N-terminal cytoplasmic region contains a PAS domain (residues 1-135), which has a very similar overall structure to PAS domains in other proteins (7). The Kv11.1a PAS domain contains an N-terminal Cap (residues , the PAS core (residues 26 -75), a connector helix (residues 76 -87), and a ␤-scaffold region (residues 88 -135).…”