Histidine protein kinases: key signal transducers outside the animal kingdom

Abstract

Histidine protein kinases (HPKs) are a large family of signal-transduction enzymes that autophosphorylate on a conserved histidine residue. HPKs form two-component signaling systems together with their downstream target proteins, the response regulators, which have a conserved aspartate in a so-called 'receiver domain' that is phosphorylated by the HPK. Two-component signal transduction is prevalent in bacteria and is also widely used by eukaryotes outside the animal kingdom. The typical HPK is a transmembrane receptor with an amino-terminal extracellular sensing domain and a carboxy-terminal cytosolic signaling domain; most, if not all, HPKs function as dimers. They show little similarity to protein kinases that phosphorylate serine, threonine or tyrosine residues, but may share a distant evolutionary relationship with these enzymes. In excess of a thousand known genes encode HPKs, which are important for multiple functions in bacteria, including chemotaxis and quorum sensing, and in eukaryotes, including hormone-dependent developmental processes. The proteins divide into at least 11 subfamilies, only one of which is present in eukaryotes, suggesting that lateral gene transfer gave rise to two-component signaling in these organisms.

Figure 1

Conserved sequence motifs in the 11 histidine protein kinase subfamilies. (a) Motifs representative of conserved sequences in the HPK1 family, which includes a majority of all HPKs, including all eukaryotic HPKs [1]. (b) The relative positions of the conserved motifs in a representative HPK (E. coli EnvZ). Regions known or predicted to be α helical are shown as rectangles, and β sheets as arrows [14,21]. The conserved regions that make up the HPK core, designated the H, N, D, F and G boxes (shown in blue), typically span approximately 200 residues in total [1,19]. HAMP is a linker domain, and TM1 and TM2 are transmembrane helices. Sequence alignments of (c) the H box, (d) the N box, (e) the D and F boxes, and (f) the G box for one representative member of each of the 11 HPK subfamilies (except for the HPK1 family, where one member of HPK1a and one member of HPK1b are shown). The proteins used to make this alignment were: HPK1a, Pseudomonas aeruginosa KinB (595 amino acids in total); HPK1b, E. coli TorS (914 amino acids); HPK2, E. coli EnvZ (450 amino acids); HPK3, E. coli PhoQ (486 amino acids); HPK4, E. coli NtrB (349 amino acids); HPK5, E. coli DcuS (543 amino acids); HPK6, Archaeoglobus fulgidus g2648416 (607 amino acids); HPK7, E. coli NarQ (566 amino acids); HPK8, E. coli YehU (561 amino acids); HPK9, E. coli CheA (654 amino acids); HPK10, Streptococcus pneumoniae ComD (441 amino acids); HPK11, Methanobacterium mth292 (564 amino acids). The regions chosen for these alignments were taken from subfamily-specific alignments carried out in one of our previous studies [1], and are indicated in parentheses. Sequences were aligned using ClustalW. To simplify the alignment, a 25 amino-acid region of HPK9 was removed in the D-box region (indicated by an open square), and a 3 amino-acid region of HPK8 was removed in the G-box region (indicated by a filled square). HPK9 does not contain an H box in its dimerization domain, so HPK9 was left out of the H-box alignment. HPK7 and HPK8 do not contain an F box. The HPK11 subfamily contains a partially conserved F box, but the example used for this alignment does not. Highly conserved residues (those present in a majority of the subfamilies) are shown boxed in dark blue, and a consensus sequence is presented below the aligned sequences; positions containing chemically similar residues are shown boxed in light blue and indicated by a dot in the consensus sequence.

Figure 2

A comparison of the three-dimensional structures of three HPK families (HPK2, HPK3, and HPK9) shows the strong conservation of the catalytic domain structure. (a) The kinase core (dimerization and catalytic domains) of an HPK9, the Thermotoga maritima CheA (Protein Data Bank, PDB, entry 1B3Q) [15]. (b) The catalytic domain of T. maritima CheA complexed with Mg²⁺ and the nucleotide analog ADPCP (PDB entry 1I58) [16]. (c) The catalytic domain of the HPK2 E. coli EnvZ complexed with ADP (model 1 from PDB entry 1BXD) [14]. (d) The catalytic domain of an HPK3, PhoQ of E. coli, complexed with Mg²⁺ and the nucleotide analog AMPNP (PDB entry 1ID0) [18]. The figure was created with Swiss-PdbViewer 3.7 and rendered with POV-Ray 3.1.