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. 2013 Oct 9;4(10):793–801. doi: 10.1007/s13238-013-3915-y

Structural basis for a homodimeric ATPase subunit of an ECF transporter

Chengliang Chai 1,3, You Yu 2, Wei Zhuo 2, Haifeng Zhao 2, Xiaolu Li 2, Na Wang 2, Jijie Chai 1,2, Maojun Yang 2,
PMCID: PMC4875438  PMID: 24104393

Abstract

The transition metal cobalt, an essential cofactor for many enzymes in prokaryotes, is taken up by several specific transport systems. The CbiMNQO protein complex belongs to type-1 energy-coupling factor (ECF) transporters and is a widespread group of microbial cobalt transporters. CbiO is the ATPase subunit (A-component) of the cobalt transporting system in the gram-negative thermophilic bacterium Thermoanaerobacter tengcongensis. Here we report the crystal structure of a nucleotide-free CbiO at a resolution of 2.3 Å. CbiO contains an N-terminal canonical nucleotide-binding domain (NBD) and C-terminal helical domain. Structural and biochemical data show that CbiO forms a homodimer mediated by the NBD and the C-terminal domain. Interactions mainly via conserved hydrophobic amino acids between the two C-terminal domains result in formation of a four-helix bundle. Structural comparison with other ECF transporters suggests that non-conserved residues outside the T-component binding groove in the A component likely act as a specificity determinant for T components. Together, our data provide information on understanding of the structural organization and interaction of the CbiMNQO system.

Keywords: CbiO, Cobalt, ECF, ATPase, Thermoanaerobactertengcongensis

Footnotes

These authors contributed equally to the work.

References

  1. Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, Mc-Coy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr. 2002;58:1948–1954. doi: 10.1107/S0907444902016657. [DOI] [PubMed] [Google Scholar]
  2. Berntsson RP, ter Beek J, Majsnerowska M, Duurkens RH, Puri P, Poolman B, Slotboom DJ. Structural divergence of paralogous S components from ECF-type ABC transporters. Proc Natl Acad Sci U S A. 2012;109:13990–13995. doi: 10.1073/pnas.1203219109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chen J, Lu G, Lin J, Davidson AL, Quiocho FA. A tweezers-like motion of the ATP-binding cassette dimer in an ABC transport cycle. Mol Cell. 2003;12:651–661. doi: 10.1016/j.molcel.2003.08.004. [DOI] [PubMed] [Google Scholar]
  4. Collaborative Computational Project, N. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr. 1994;50:760–763. doi: 10.1107/S0907444994003112. [DOI] [PubMed] [Google Scholar]
  5. Dean M, Allikmets R. Evolution of ATP-binding cassette transporter genes. Curr Opin Genet Dev. 1995;5:779–785. doi: 10.1016/0959-437X(95)80011-S. [DOI] [PubMed] [Google Scholar]
  6. Dean M, Hamon Y, Chimini G. The human ATP-binding cassette (ABC) transporter superfamily. J Lipid Res. 2001;42:1007–1017. [PubMed] [Google Scholar]
  7. Eitinger T, Suhr J, Moore L, Smith JA. Secondary transporters for nickel and cobalt ions: theme and variations. Biometals. 2005;18:399–405. doi: 10.1007/s10534-005-3714-x. [DOI] [PubMed] [Google Scholar]
  8. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr. 2004;60:2126–2132. doi: 10.1107/S0907444904019158. [DOI] [PubMed] [Google Scholar]
  9. Erkens GB, Berntsson RP, Fulyani F, Majsnerowska M, Vujicic-Zagar A, Ter Beek J, Poolman B, Slotboom DJ. The structural basis of modularity in ECF-type ABC transporters. Nat Struct Mol Biol. 2011;18:755–760. doi: 10.1038/nsmb.2073. [DOI] [PubMed] [Google Scholar]
  10. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17:368–376. doi: 10.1007/BF01734359. [DOI] [PubMed] [Google Scholar]
  11. Finkenwirth F, Neubauer O, Gunzenhauser J, Schoknecht J, Scolari S, Stockl M, Korte T, Herrmann A, Eitinger T. Subunit composition of an energy-coupling-factor-type biotin transporter analysed in living bacteria. Biochem J. 2010;431:373–380. doi: 10.1042/BJ20100813. [DOI] [PubMed] [Google Scholar]
  12. Fisher DJ, Fernandez RE, Adams NE, Maurelli AT. Uptake of biotin by Chlamydia Spp. through the use of a bacterial transporter (BioY) and a host-cell transporter (SMVT) PLoS One. 2012;7:e46052. doi: 10.1371/journal.pone.0046052. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hung LW, Wang IX, Nikaido K, Liu PQ, Ames GF, Kim SH. Crystal structure of the ATP-binding subunit of an ABC transporter. Nature. 1998;396:703–707. doi: 10.1038/25393. [DOI] [PubMed] [Google Scholar]
  14. Karpowich NK, Wang DN. Assembly and mechanism of a group II ECF transporter. Proc Natl Acad Sci U S A. 2013;110:2534–2539. doi: 10.1073/pnas.1217361110. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kirsch F, Frielingsdorf S, Pohlmann A, Ziomkowska J, Herrmann A, Eitinger T. Essential amino acid residues of BioY reveal that dimers are the functional S unit of the Rhodobacter capsulatus biotin transporter. J Bacteriol. 2012;194:4505–4512. doi: 10.1128/JB.00683-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Korkhov VM, Mireku SA, Locher KP. Structure of AMP-PNP-bound vitamin B12 transporter BtuCD-F. Nature. 2012;490:367–372. doi: 10.1038/nature11442. [DOI] [PubMed] [Google Scholar]
  17. Li X, Zhuo W, Yu J, Ge J, Gu J, Feng Y, Yang M, Wang L, Wang N. Structure of the nucleotide-binding domain of a dipeptide ABC transporter reveals a novel iron-sulfur clusterbinding domain. Acta Crystallogr D Biol Crystallogr. 2013;69:256–265. doi: 10.1107/S0907444912045180. [DOI] [PubMed] [Google Scholar]
  18. Majsnerowska M, Hanelt I, Wunnicke D, Schafer LV, Steinhoff HJ, Slotboom DJ. Substrate-induced conformational changes in the S-component ThiT from an energy coupling factor transporter. Structure. 2013;21:861–867. doi: 10.1016/j.str.2013.03.007. [DOI] [PubMed] [Google Scholar]
  19. Mulrooney SB, Hausinger RP. Nickel uptake and utilization by microorganisms. FEMS Microbiol Rev. 2003;27:239–261. doi: 10.1016/S0168-6445(03)00042-1. [DOI] [PubMed] [Google Scholar]
  20. Neubauer O, Alfandega A, Schoknecht J, Sternberg U, Pohlmann A, Eitinger T. Two essential arginine residues in the T components of energy-coupling factor transporters. J Bacteriol. 2009;191:6482–6488. doi: 10.1128/JB.00965-09. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Neubauer O, Reiffler C, Behrendt L, Eitinger T. Interactions among the A and T units of an ECF-type biotin transporter analyzed by site-specific crosslinking. PLoS One. 2011;6:e29087. doi: 10.1371/journal.pone.0029087. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Method Enzymol. 1997;276:307–326. doi: 10.1016/S0076-6879(97)76066-X. [DOI] [PubMed] [Google Scholar]
  23. Rodionov DA, Hebbeln P, Gelfand MS, Eitinger T. Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATPbinding cassette transporters. J Bacteriol. 2006;188:317–327. doi: 10.1128/JB.188.1.317-327.2006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Scheffel F, Demmer U, Warkentin E, Hulsmann A, Schneider E, Ermler U. Structure of the ATPase subunit CysA of the putative sulfate ATP-binding cassette (ABC) transporter from Alicyclobacillus acidocaldarius. FEBS Lett. 2005;579:2953–2958. doi: 10.1016/j.febslet.2005.04.017. [DOI] [PubMed] [Google Scholar]
  25. Siche S, Neubauer O, Hebbeln P, Eitinger T. A bipartite S unit of an ECF-type cobalt transporter. Res Microbiol. 2010;161:824–829. doi: 10.1016/j.resmic.2010.09.010. [DOI] [PubMed] [Google Scholar]
  26. Story RM, Weber IT, Steitz TA. The structure of the E. coli recA protein monomer and polymer. Nature. 1992;355:318–325. doi: 10.1038/355318a0. [DOI] [PubMed] [Google Scholar]
  27. ter Beek J, Duurkens RH, Erkens GB, Slotboom DJ. Quaternary structure and functional unit of energy coupling factor (ECF)-type transporters. J Biol Chem. 2011;286:5471–5475. doi: 10.1074/jbc.M110.199224. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Verdon G, Albers SV, Dijkstra BW, Driessen AJ, Thunnissen AM. Crystal structures of the ATPase subunit of the glucose ABC transporter from Sulfolobus solfataricus: nucleotidefree and nucleotide-bound conformations. J Mol Biol. 2003;330:343–358. doi: 10.1016/S0022-2836(03)00575-8. [DOI] [PubMed] [Google Scholar]
  29. Wang T, Fu G, Pan X, Wu J, Gong X, Wang J, Shi Y. Structure of a bacterial energy-coupling factor transporter. Nature. 2013;497:272–276. doi: 10.1038/nature12045. [DOI] [PubMed] [Google Scholar]
  30. Xu K, Zhang M, Zhao Q, Yu F, Guo H, Wang C, He F, Ding J, Zhang P. Crystal structure of a folate energy-coupling factor transporter from Lactobacillus brevis. Nature. 2013;497:268–271. doi: 10.1038/nature12046. [DOI] [PubMed] [Google Scholar]
  31. Zhang P, Wang J, Shi Y. Structure and mechanism of the S component of a bacterial ECF transporter. Nature. 2010;468:717–720. doi: 10.1038/nature09488. [DOI] [PubMed] [Google Scholar]

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