Stewart, V and Chen, LL (2010) The S helix mediates signal transmission as a HAMP domain coiled-coil extension in the NarX nitrate sensor from Escherichia coli K-12. J. Bacteriol. 192:734-45
In the nitrate-responsive, homodimeric NarX sensor, two cytoplasmic membrane alpha-helices delimit the periplasmic ligand-binding domain. The HAMP domain, a four-helix parallel coiled-coil built from two alpha-helices (HD1 and HD2), immediately follows the second transmembrane helix. Previous computational studies identified a likely coiled-coil-forming alpha-helix, the signaling helix (S helix), in a range of signaling proteins, including eucaryal receptor guanylyl cyclases, but its function remains obscure. In NarX, the HAMP HD2 and S-helix regions overlap and apparently form a continuous coiled-coil marked by a heptad repeat stutter discontinuity at the distal boundary of HD2. Similar composite HD2-S-helix elements are present in other sensors, such as Sln1p from Saccharomyces cerevisiae. We constructed deletions and missense substitutions in the NarX S helix. Most caused constitutive signaling phenotypes. However, strongly impaired induction phenotypes were conferred by heptad deletions within the S-helix conserved core and also by deletions that remove the heptad stutter. The latter observation illuminates a key element of the dynamic bundle hypothesis for signaling across the heptad stutter adjacent to the HAMP domain in methyl-accepting chemotaxis proteins (Q. Zhou, P. Ames, and J. S. Parkinson, Mol. Microbiol. 73:801-814, 2009). Sequence comparisons identified other examples of heptad stutters between a HAMP domain and a contiguous coiled-coil-like heptad repeat sequence in conventional sensors, such as CpxA, EnvZ, PhoQ, and QseC; other S-helix-containing sensors, such as BarA and TorS; and the Neurospora crassa Nik-1 (Os-1) sensor that contains a tandem array of alternating HAMP and HAMP-like elements. Therefore, stutter elements may be broadly important for HAMP function.
Amino Acid Sequence; Bacterial Outer Membrane Proteins/chemistry; Bacterial Outer Membrane Proteins/genetics; Bacterial Outer Membrane Proteins/physiology; Bacterial Proteins/chemistry; Bacterial Proteins/genetics; Bacterial Proteins/physiology; Escherichia coli Proteins/chemistry; Escherichia coli Proteins/genetics; Escherichia coli Proteins/physiology; Membrane Proteins/chemistry; Membrane Proteins/genetics; Membrane Proteins/physiology; Molecular Sequence Data; Multienzyme Complexes/chemistry; Multienzyme Complexes/genetics; Multienzyme Complexes/physiology; Mutagenesis, Site-Directed; Phenotype; Phosphotransferases/chemistry; Phosphotransferases/genetics; Phosphotransferases/physiology; Protein Kinases/chemistry; Protein Kinases/genetics; Protein Kinases/physiology; Protein Structure, Secondary; Protein Structure, Tertiary/genetics; Protein Structure, Tertiary/physiology; Sequence Homology, Amino Acid; Signal Transduction; Structure-Activity Relationship
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