Structural modeling of a novel membrane-bound globin-coupled sensor in Geobacter sulfurreducens

Dietmar Hammerschmid; Francesca Germani; Salvador I Drusin; Charline Fagnen; Claudio D Schuster; David Hoogewijs; Marcelo A Marti; Catherine Venien-Bryan; Luc Moens; Sabine Van Doorslaer; Frank Sobott; Sylvia Dewilde

doi:10.1016/j.csbj.2021.03.031

Structural modeling of a novel membrane-bound globin-coupled sensor in Geobacter sulfurreducens

Comput Struct Biotechnol J. 2021 Mar 26:19:1874-1888. doi: 10.1016/j.csbj.2021.03.031. eCollection 2021.

Authors

Affiliations

¹ Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
² Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
³ Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina.
⁴ Sorbonne Université, UMR 7590, CNRS, Muséum National d'Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France.
⁵ Section of Medicine, Department of Endocrinology, Metabolism and Cardiovascular System, University of Fribourg, Switzerland.
⁶ Biophysics and Biomedical Physics, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
⁷ Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
⁸ School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom.

Abstract

Globin-coupled sensors (GCS) usually consist of three domains: a sensor/globin, a linker, and a transmitter domain. The globin domain (GD), activated by ligand binding and/or redox change, induces an intramolecular signal transduction resulting in a response of the transmitter domain. Depending on the nature of the transmitter domain, GCSs can have different activities and functions, including adenylate and di-guanylate cyclase, histidine kinase activity, aerotaxis and/or oxygen sensing function. The gram-negative delta-proteobacterium Geobacter sulfurreducens expresses a protein with a GD covalently linked to a four transmembrane domain, classified, by sequence similarity, as GCS (GsGCS). While its GD is fully characterized, not so its transmembrane domain, which is rarely found in the globin superfamily. In the present work, GsGCS was characterized spectroscopically and by native ion mobility-mass spectrometry in combination with cryo-electron microscopy. Although lacking high resolution, the oligomeric state and the electron density map were valuable for further rational modeling of the full-length GsGCS structure. This model demonstrates that GsGCS forms a transmembrane domain-driven tetramer with minimal contact between the GDs and with the heme groups oriented outward. This organization makes an intramolecular signal transduction less likely. Our results, including the auto-oxidation rate and redox potential, suggest a potential role for GsGCS as redox sensor or in a membrane-bound e^-/H⁺ transfer. As such, GsGCS might act as a player in connecting energy production to the oxidation of organic compounds and metal reduction. Database searches indicate that GDs linked to a four or seven helices transmembrane domain occur more frequently than expected.

Keywords: AfGcHK, Anaeromyxobacter sp. Fw109-5 GcHK; AsFRMF, Ascaris suum FRMF-amide receptor; AvGReg, Azotobacter vinilandii Greg; BpGReg, Bordetella pertussis Greg; BsHemAT, Bacillus subtilis HemAT; CCS, collision cross section; CIU, collision-induced unfolding; CMC, critical micelle concentration; CV, cyclic voltammetry; CeGLB26, Caenorhabditis elegans globin 26; CeGLB33, Caenorhabditis elegans globin 33; CeGLB6, Caenorhabditis elegans globin 6; DDM, n-dodecyl-β-d-maltoside; DPV, differential pulse voltammetry; EcDosC, Escherichia coli Dos with DGC activity; FMRF, H-Phe-Met-Arg-Phe-NH2 neuropeptide; GCS, globin-coupled sensor; GD, globin domain; GGDEF, Gly-Gly-Asp-Glu-Phe motive; Gb, globin; Geobacter sulfurreducens; GintHb, hemoglobin from Gasterophilus intestinalis; Globin-coupled sensor; GsGCS, Geobacter sulfurreducens GCS; GsGCS162, GD of GsGCS; IM-MS, ion mobility-mass spectrometry; LmHemAC, Leishmania major HemAC; MaPgb, Methanosarcina acetivorans protoglobin; MtTrHbO, Mycobacterium tuberculosis truncated hemoglobin O; NH4OAc, ammonium acetate; OG, n-octyl-β-d-glucopyranoside; PDE, phosphodiesterase; PcMb, Physether catodon myoglobin; PccGCS, Pectobacterium carotivorum GCS; PsiE, phosphate-starvation-inducible E; RR, resonance Raman; SCE, saturated calomel electrode; SHE, standard hydrogen electrode; SaktrHb, Streptomyces avermitilis truncated hemoglobin-antibiotic monooxygenase; SwMb, myoglobin from sperm whale; TD, Transmitter domain; TmD, Transmembrane domain; Transmembrane domain; Transmembrane-coupled globins; mNgb, mouse neuroglobin.