Heme-based globin-coupled oxygen sensors: linking oxygen binding to functional regulation of diguanylate cyclase, histidine kinase, and methyl-accepting chemotaxis

Abstract

An emerging class of novel heme-based oxygen sensors containing a globin fold binds and senses environmental O2 via a heme iron complex. Structure-function relationships of oxygen sensors containing a heme-bound globin fold are different from those containing heme-bound PAS and GAF folds. It is thus worth reconsidering from an evolutionary perspective how heme-bound proteins with a globin fold similar to that of hemoglobin and myoglobin could act as O2 sensors. Here, we summarize the molecular mechanisms of heme-based oxygen sensors containing a globin fold in an effort to shed light on the O2-sensing properties and O2-stimulated catalytic enhancement observed for these proteins.

Keywords: Chemotaxis; Cyclic GMP (cGMP); Heme; Hemoglobin; Histidine Kinases; Myoglobin; Oxygen Binding.

FIGURE 1.

Alignment of heme-bound oxygen-sensing and functional domains of the heme-based oxygen sensors. Left, the C-terminal HK domain in the two-component system containing N-terminal heme-bound globin, PAS, or GAF domains. Right, the C-terminal functional domains associated with MCP, c-diGMP homeostasis (DGC, synthesis; and PDE, degradation), and unknown functions (transmembrane (TM)) containing the N-terminal heme-bound globin or PAS domain. GCSs are defined as chimeric proteins composed of heme-bound globin and functional domains (–18). Note that EcDOS and FixL have two tandem PAS domains; the heme iron complex is bound to the first PAS domain in EcDOS and to the second PAS domain in FixL. Similarly, DevS and DosT have two tandem GAF domains; in both cases, the heme iron complex is bound to the first GAF domain. Note that globin folds are not always localized at the N terminus but are inserted into diverse regions, as predicted from the amino acid sequences of sensor globins that are yet to be characterized (–18). AxPDEA1, A. xylinum PDEA1.

FIGURE 2.

A, c-diGMP is an important second messenger in bacteria. Synthesis (DGC) and linearization (PDE) of c-diGMP, an important second messenger in numerous physiological functions (including biofilm formation), in E. coli are conducted by the heme-based oxygen sensor enzymes YddV and EcDOS, respectively. YddV is a GCS, whereas EcDOS is a heme-bound protein with a PAS fold. O₂ binding to the heme Fe(II) complexes of these enzymes enhances catalysis to a significant extent. However, because the O₂ affinities of the two enzymes are markedly different (5–20-fold) from each other, each enzyme functions to accommodate the local O₂ concentration in response to stimuli to maintain c-diGMP homeostasis. This figure is adapted from Ref. . B, schematic mechanism of AfGcHK (a GCS) of a two-component system. O₂ binding to the heme Fe(II) complex, which is bound to the N-terminal domain via the globin fold, significantly stimulates the C-terminal domain of HK, resulting in autophosphorylation of AfGcHK. Once autophosphorylated, AfGcHK transfers the phosphate group to the cognate response regulator. Although, the enzyme is depicted here as a monomer for the sake of simplicity, all HKs reported to date, including AfGcHK, are dimers (or tetramers). It has been suggested that autophosphorylation is exerted “crosswise” such that the kinase in one subunit phosphorylates the His residue of HK in the other subunit of the dimer (or tetramer). aa, amino acids; Rec, receiver domain. This figure is adapted from Ref. .

FIGURE 3.

A, heme environmental structures of GCSs and sperm whale Mb. Left, the heme Fe(III)-CN⁻ complex of HemAT-Bs (Protein Data Bank code 1OR4) (22). Center, the heme Fe(III) complex of GsGCS (code 2W31) (19). Right, the heme Fe(II)-O₂ complex of sperm whale (SW) Mb (code 1A6M) (98). Note that HemAT-Bs and GsGCS are GCSs, whereas sperm whale Mb is a vertebrate globin. The color of the helix corresponds to helix notification in Fig. 3B. Distal B- and E- and proximal F-helices are shown in orange, green, and light blue, respectively. B, alignment of amino acid sequences of selected GCSs and sperm whale Mb with helix notification. Helix notification was based on sperm whale Mb and HemAT (–16, 38, 98). The distal Tyr residue (B10), which binds to O₂ in the heme Fe(II)-O₂ complex, and the proximal His residue (F8) as a heme-binding site of GCS are shown in blue and red, respectively. The distal His residue (E7) interacting with O₂ in the heme Fe(II)-O₂ complex of sperm whale Mb is shown in green.