The HAMP Domain Structure Implies Helix Rotation in Transmembrane Signaling

Abstract

HAMP domains connect extracellular sensory with intracellular signaling domains in over 7500 proteins, including histidine kinases, adenylyl cyclases, chemotaxis receptors, and phosphatases. The solution structure of an archaeal HAMP domain shows a homodimeric, four-helical, parallel coiled coil with unusual interhelical packing, related to the canonical packing by rotation of the helices. This suggests a model for the mechanism of signal transduction, in which HAMP alternates between the observed conformation and a canonical coiled coil. We explored this mechanism in vitro and in vivo using HAMP domain fusions with a mycobacterial adenylyl cyclase and an E. coli chemotaxis receptor. Structural and functional studies show that the equilibrium between the two forms is dependent on the side-chain size of residue 291, which is alanine in the wild-type protein.

Bacterial chemoreceptors: high-performance signaling in networked arrays

“…Typically, HAMP domains are located between transmembrane and cytoplasmic signaling regions of known or putative transmembrane receptors, consistent with a role in converting ligand-induced conformational changes into kinase-controlling signals. In the recently solved HAMP structure each subunit contributes two amphiphilic helices (AS-1, AS-2), joined by a connector, to form a homodimeric, parallel, fourhelix bundle [43]. The sequence locations, and the exposed and buried faces of these helices, are the same as identified previously by cysteine-scanning of an intact chemoreceptor [44], and the length of the domain is close to that deduced by analysis with electron microscopy [41].…”

“…This module is a HAMP (present in histidine kinases, adenylyl kinases, methyl-accepting chemotaxis proteins and phosphatases [42]) domain and the signaling helix connects specifically to its N-terminal (AS-1) helix. The parallel four-helix structure shown is a hypothetical model, based on a recent structure of a HAMP fragment from an atypical, archaeal protein of unknown function [43], which has not yet been tested in a full-length chemoreceptor.…”

“…A recent advance comes from nuclear magnetic resonance (NMR) characterization of an isolated HAMP domain from an archaeal, hyperthermophilic, transmembrane protein of unknown function [43] (Box 3). HAMP domains, characterized by two amphiphilic helices joined by a linker [44], occur in many bacterial signaling proteins [42,45].…”

“…Sequence conservation is more subtle among HAMP modules [42,45] but 3D structure is probably shared for the approximately two-thirds of all chemoreceptors that contain the module [43]. There is substantial variation in the sequence and in the deduced 3D organization among transmembrane sensing modules, but the antiparallel four-helix bundle seems to be the most common structure [65] and this structure can be conserved even with minimal sequence identity [66].…”

“…This module is a HAMP (present in histidine kinases, adenylyl kinases, methyl-accepting chemotaxis proteins and phosphatases [42]) domain and the signaling helix connects specifically to its N-terminal (AS-1) helix. The parallel four-helix structure shown is a hypothetical model, based on a recent structure of a HAMP fragment from an atypical, archaeal protein of unknown function [43], which has not yet been tested in a full-length chemoreceptor.The 'kinase control module' is a continuous four-helix, anti-parallel coiled-coil containing two helices from each subunit, with a hairpin turn at its membrane-distal end. The adaptation region contains sites of adaptational modification, specifically surface glutamates, or glutamines deamidated to become glutamates, located midway along the ~250Å coiled-coil ( Figure I).…”