TCDB is operated by the Saier Lab Bioinformatics Group

1.A.30 The H+- or Na+-translocating Bacterial Flagellar Motor/ExbBD Outer Membrane Transport Energizer (Mot-Exb) Superfamily

The Mot-Exb Superfamily consists of six distant families, each probably with a distinct physiological function, although all may function as H+/Na+ channels, driving an energy-requiring process. The MotAB family energizes bacterial flagellar rotation while the ExbBD family energizes accumulation of large molecules (i.e. iron-siderophores, vitamin B12, DNA from phage, and colicins) from the external medium across the outer Gram-negative bacterial membrane into the periplasm. The AglRS system powers gliding motility while the SilAB systems energize gian adhesin export.  The function of a 5th family (TC# 1.A.30.5) is not known, but the ZorAB systems have been reported to function as parts of antiphage defense systems. The pmf (or smf) is probably the driving force in all cases. MotAB and PomAB are homologous to ExbBD and TolQR. MotAB of E. coli, the stator, is known to form a proton channel. This stator is composed of MotA and MotB proteins, which form a hetero-hexameric complex with a stoichiometry of four MotA and two MotB molecules. MotA can form a tetramer in the absence of MotB (Takekawa et al. 2016).

Yonekura et al. (2011) presented the first three-dimensional structure of the PomAB torque-generating stator unit analyzed by electron microscopy. The structure of PomAB revealed two arm domains, which contain the PG-binding site, connected to a large base made of the transmembrane and cytoplasmic domains. The arms lean downward to the membrane surface, likely representing a 'plugged' conformation, which would prevent ions leaking through the channel. They propose a model for how PomAB units are placed around the flagellar basal body to function as torque generators. 

Leu46 of MotB acts as the gate for hydronium ion permeation, which induces the formation of a water wire that may mediate the proton transfer to Asp32 on MotB. The free energy barrier for H3O+ permeation is consistent with the proton transfer rate deduced from the flagellar rotational speed and the number of protons per rotation, suggesting that gating is the rate-limiting step (Nishihara and Kitao 2015). Structure and dynamics of MotA/B with nonprotonated and protonated Asp32 suggested size-dependent ion selectivity. In MotA/B with the nonprotonated Asp32, the A3 segment in MotA maintains a kink whereas protonation induces a straighter shape. Assuming that the cytoplasmic domain not included in the atomic model moves as a rigid body, the protonation/deprotonation of Asp32 is inferred to induce a ratchet motion of the cytoplasmic domain, correlated with the motion of the flagellar rotor (Nishihara and Kitao 2015). 

ExbBD forms both hexameric and pentameric complexes that coexist, with the proportion of the hexamers increasing with pH. Channel current measurements and 2D crystallography thus support the existence of and transition between the two oligomeric states in membranes. The hexameric complex consists of six ExbB subunits and three ExbD transmembrane helices enclosed within the central channel (Maki-Yonekura et al. 2018).

References associated with 1.A.30 family:

Bulathsinghala, C.M., B. Jana, K.R. Baker, and K. Postle. (2013). ExbB cytoplasmic loop deletions cause immediate, proton motive force-independent growth arrest. J. Bacteriol. 195: 4580-4591. 23913327
Castillo, D.J., S. Nakamura, Y.V. Morimoto, Y.S. Che, N. Kami-Ike, S. Kudo, T. Minamino, and K. Namba. (2013). The C-terminal periplasmic domain of MotB is responsible for load-dependent control of the number of stators of the bacterial flagellar motor. Biophysics (Nagoya-shi) 9: 173-181. 27493556
Doron, S., S. Melamed, G. Ofir, A. Leavitt, A. Lopatina, M. Keren, G. Amitai, and R. Sorek. (2018). Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359:. 29371424
Hosking, E.R., C. Vogt, E.P. Bakker, and M.D. Manson. (2006). The Escherichia coli MotAB proton channel unplugged. J. Mol. Biol. 364: 921-937. 17052729
Ito, M., D.B. Hicks, T.M. Henkin, A.A. Guffanti, B.D. Powers, L. Zvi, K. Uematsu, and T.A. Krulwich. (2004). MotPS is the stator-force generator for motility of alkaliphilic Bacillus, and its homologue is a second functional Mot in Bacillus subtilis. Mol. Microbiol. 53: 1035-1049. 15306009
Jakobczak, B., D. Keilberg, K. Wuichet, and L. Søgaard-Andersen. (2015). Contact- and Protein Transfer-Dependent Stimulation of Assembly of the Gliding Motility Machinery in Myxococcus xanthus. PLoS Genet 11: e1005341. 26132848
Kitao, A. and Y. Nishihara. (2017). Structure of the MotA/B Proton Channel. Methods Mol Biol 1593: 133-145. 28389950
Klebba, P.E. (2016). ROSET Model of TonB Action in Gram-Negative Bacterial Iron Acquisition. J. Bacteriol. 198: 1013-1021. 26787763
Koerdt, A., A. Paulick, M. Mock, K. Jost, and K.M. Thormann. (2009). MotX and MotY are required for flagellar rotation in Shewanella oneidensis MR-1. J. Bacteriol. 191: 5085-5093. 19502394
Kojima, S., K. Imada, M. Sakuma, Y. Sudo, C. Kojima, T. Minamino, M. Homma, and K. Namba. (2009). Stator assembly and activation mechanism of the flagellar motor by the periplasmic region of MotB. Mol. Microbiol. 73: 710-718. 19627504
Liew, C.W., R.M. Hynson, L.A. Ganuelas, N. Shah-Mohammadi, A.P. Duff, S. Kojima, M. Homma, and L.K. Lee. (2017). Solution structure analysis of the periplasmic region of bacterial flagellar motor stators by small angle X-ray scattering. Biochem. Biophys. Res. Commun. [Epub: Ahead of Print] 29197577
Lo, C.J., Y. Sowa, T. Pilizota, and R.M. Berry. (2013). Mechanism and kinetics of a sodium-driven bacterial flagellar motor. Proc. Natl. Acad. Sci. USA 110: E2544-2551. 23788659
Maki-Yonekura, S., R. Matsuoka, Y. Yamashita, H. Shimizu, M. Tanaka, F. Iwabuki, and K. Yonekura. (2018). Hexameric and pentameric complexes of the ExbBD energizer in the Ton system. Elife 7:. 29661272
Mignot, T. and M. Nöllmann. (2017). New insights into the function of a versatile class of membrane molecular motors from studies of Myxococcus xanthus surface (gliding) motility. Microb Cell 4: 98-100. 28357395
Nan, B., J. Chen, J.C. Neu, R.M. Berry, G. Oster, and D.R. Zusman. (2011). Myxobacteria gliding motility requires cytoskeleton rotation powered by proton motive force. Proc. Natl. Acad. Sci. USA 108: 2498-2503. 21248229
Nishihara Y. and Kitao A. (2015). Gate-controlled proton diffusion and protonation-induced ratchet motion in the stator of the bacterial flagellar motor. Proc Natl Acad Sci U S A. 112(25):7737-42. 26056313
O'Neill, J., M. Xie, M. Hijnen, and A. Roujeinikova. (2011). Role of the MotB linker in the assembly and activation of the bacterial flagellar motor. Acta Crystallogr D Biol Crystallogr 67: 1009-1016. 22120737
O'Neill, J., M. Xie, M. Hijnen, and A. Roujeinikova. (2011). Role of the MotB linker in the assembly and activation of the bacterial flagellar motor. Acta Crystallogr D Biol Crystallogr 67: 1009-1016. 18540076
Okabe, M., T. Yakushi, and M. Homma. (2005). Interactions of MotX with MotY and with the PomA/PomB sodium ion channel complex of the Vibrio alginolyticus polar flagellum. J. Biol. Chem. 280: 25659-25664. 15866878
Rassam, P., K.R. Long, R. Kaminska, D.J. Williams, G. Papadakos, C.G. Baumann, and C. Kleanthous. (2018). Intermembrane crosstalk drives inner-membrane protein organization in Escherichia coli. Nat Commun 9: 1082. 29540681
Takekawa, N., N. Terahara, T. Kato, M. Gohara, K. Mayanagi, A. Hijikata, Y. Onoue, S. Kojima, T. Shirai, K. Namba, and M. Homma. (2016). The tetrameric MotA complex as the core of the flagellar motor stator from hyperthermophilic bacterium. Sci Rep 6: 31526. 27531865
Wille T., Wagner C., Mittelstadt W., Blank K., Sommer E., Malengo G., Dohler D., Lange A., Sourjik V., Hensel M. and Gerlach RG. (2014). SiiA and SiiB are novel type I secretion system subunits controlling SPI4-mediated adhesion of Salmonella enterica. Cell Microbiol. 16(2):161-78. 24119191
Yonekura, K., S. Maki-Yonekura, and M. Homma. (2011). Structure of the flagellar motor protein complex PomAB: implications for the torque-generating conformation. J. Bacteriol. 193: 3863-3870. 21642461
Zhu S., Homma M. and Kojima S. (2012). Intragenic suppressor of a plug deletion nonmotility mutation in PotB, a chimeric stator protein of sodium-driven flagella. J Bacteriol. 194(24):6728-35. 23024347