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Structural characterization of the putative ABC-type 2 transporter from Thermotoga maritima MSB8

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Journal of Structural and Functional Genomics

Abstract

This study describes the structure of the putative ABC-type 2 transporter TM0543 from Thermotoga maritima MSB8 determined at a resolution of 2.3 Å. In comparative sequence-clustering analysis, TM0543 displays similarity to NatAB-like proteins, which are components of the ABC-type Na+ efflux pump permease. However, the overall structure fold of the predicted nucleotide-binding domain reveals that it is different from any known structure of ABC-type efflux transporters solved to date. The structure of the putative TM0543 domain also exhibits different dimer architecture and topology of its presumed ATP binding pocket, which may indicate that it does not bind nucleotide at all. Structural analysis of calcium ion binding sites found at the interface between TM0543 dimer subunits suggests that protein may be involved in ion-transporting activity. A detailed analysis of the protein sequence and structure is presented and discussed.

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Fig. 1
Fig. 2

Abbreviations

TMD:

Transmembrane domain

ATP-BD:

Nucleotide-binding domain

TM:

Transmembrane α-helix

ABC Superfamily:

ATP-binding Cassette Superfamily

TCDB:

Transport Classification Database (http://www.tcdb.org/)

PDB:

Protein Data Bank

References

  1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  2. An J, Nakama T, Kubota Y, Sarai A (1998) 3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules. Bioinformatics 14(2):188–195

    Article  CAS  PubMed  Google Scholar 

  3. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR (2004) The Pfam protein families database. Nucleic Acids Res 32(Database issue):D138–D141

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  4. Chen J, Lu G, Lin J, Davidson AL, Quiocho FA (2003) A tweezers-like motion of the ATP-binding cassette dimer in an ABC transport cycle. Mol Cell 12(3):651–661

    Article  CAS  PubMed  Google Scholar 

  5. Cheng J, Guffanti AA, Krulwich TA (1997) A two-gene ABC-type transport system that extrudes Na+ in Bacillus subtilis is induced by ethanol or protonophore. Mol Microbiol 23(6):1107–1120

    Article  CAS  PubMed  Google Scholar 

  6. Cherezov V, Hofer N, Szebenyi DM, Kolaj O, Wall JG, Gillilan R, Srinivasan V, Jaroniec CP, Caffrey M (2008) Insights into the mode of action of a putative zinc transporter CzrB in Thermus thermophilus. Structure 16(9):1378–1388

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  7. Cowtan KD, Zhang KY (1999) Density modification for macromolecular phase improvement. Prog Biophys Mol Biol 72(3):245–270

    Article  CAS  PubMed  Google Scholar 

  8. Davidson AL, Maloney PC (2007) ABC transporters: how small machines do a big job. Trends Microbiol 15(10):448–455

    Article  CAS  PubMed  Google Scholar 

  9. Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113

    Article  PubMed Central  PubMed  Google Scholar 

  10. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 1):2126–2132

    Article  PubMed  Google Scholar 

  11. Fiser A, Sali A (2003) Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 374:461–491

    Article  CAS  PubMed  Google Scholar 

  12. Frickey T, Lupas A (2004) CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics 20(18):3702–3704

    Article  CAS  PubMed  Google Scholar 

  13. Gerber S, Comellas-Bigler M, Goetz BA, Locher KP (2008) Structural basis of trans-inhibition in a molybdate/tungstate ABC transporter. Science 321(5886):246–250

    Article  CAS  PubMed  Google Scholar 

  14. Guex N, Peitsch MC, Schwede T (2009) Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis 30(Suppl 1):S162–S173

    Article  PubMed  Google Scholar 

  15. Higgins CF (2001) ABC transporters: physiology, structure and mechanism—an overview. Res Microbiol 152(3–4):205–210

    Article  CAS  PubMed  Google Scholar 

  16. Hirokawa T, Boon-Chieng S, Mitaku S (1998) SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 14(4):378–379

    Article  CAS  PubMed  Google Scholar 

  17. Hofmann K, Stoffel W (1993) TMbase—a database of membrane spanning proteins segments. Biol Chem Hoppe-Seyler 374:166

    Google Scholar 

  18. Holland IB, Blight MA (1999) ABC-ATPases, adaptable energy generators fuelling transmembrane movement of a variety of molecules in organisms from bacteria to humans. J Mol Biol 293(2):381–399

    Article  CAS  PubMed  Google Scholar 

  19. Hollenstein K, Frei DC, Locher KP (2007) Structure of an ABC transporter in complex with its binding protein. Nature 446(7132):213–216

    Article  CAS  PubMed  Google Scholar 

  20. Holm L, Sander C (1993) Protein structure comparison by alignment of distance matrices. J Mol Biol 233(1):123–138

    Article  CAS  PubMed  Google Scholar 

  21. Hung LW, Wang IX, Nikaido K, Liu PQ, Ames GF, Kim SH (1998) Crystal structure of the ATP-binding subunit of an ABC transporter. Nature 396(6712):703–707

    Article  CAS  PubMed  Google Scholar 

  22. Hvorup RN, Goetz BA, Niederer M, Hollenstein K, Perozo E, Locher KP (2007) Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF. Science 317(5843):1387–1390

    Article  CAS  PubMed  Google Scholar 

  23. Kadaba NS, Kaiser JT, Johnson E, Lee A, Rees DC (2008) The high-affinity E. coli methionine ABC transporter: structure and allosteric regulation. Science 321(5886):250–253

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  24. Kosinski J, Cymerman IA, Feder M, Kurowski MA, Sasin JM, Bujnicki JM (2003) A “FRankenstein’s monster” approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation. Proteins 53(Suppl 6):369–379

    Article  CAS  PubMed  Google Scholar 

  25. Kurowski MA, Bujnicki JM (2003) GeneSilico protein structure prediction meta-server. Nucleic Acids Res 31(13):3305–3307

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. Laskowski RA, Watson JD, Thornton JM (2005) ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 33(Web Server issue):W89–W93

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  27. Lee SJ, Bohm A, Krug M, Boos W (2007) The ABC of binding-protein-dependent transport in Archaea. Trends Microbiol 15(9):389–397

    Article  CAS  PubMed  Google Scholar 

  28. Linton KJ (2007) Structure and function of ABC transporters. Physiology (Bethesda) 22:122–130

    Article  CAS  Google Scholar 

  29. Locher KP, Lee AT, Rees DC (2002) The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism. Science 296(5570):1091–1098

    Article  CAS  PubMed  Google Scholar 

  30. Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC (2003) Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins 50(3):437–450

    Article  CAS  PubMed  Google Scholar 

  31. Lu G, Westbrooks JM, Davidson AL, Chen J (2005) ATP hydrolysis is required to reset the ATP-binding cassette dimer into the resting-state conformation. Proc Natl Acad Sci USA 102(50):17969–17974

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  32. McNicholas S, Potterton E, Wilson KS, Noble ME (2011) Presenting your structures: the CCP4 mg molecular-graphics software. Acta Crystallogr D Biol Crystallogr 67(Pt 4):386–394

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  33. Minor W, Cymborowski M, Otwinowski Z, Chruszcz M (2006) HKL-3000: the integration of data reduction and structure solution-from diffraction images to an initial model in minutes. Acta Crystallogr D Biol Crystallogr 62(Pt 8):859–866

    Article  PubMed  Google Scholar 

  34. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53(Pt 3):240–255

    Article  CAS  PubMed  Google Scholar 

  35. Otwinowski Z (ed) (1991) MLPHARE: isomorphous replacement and anomalous scattering. In: Proceedings of the CCP4 study weekend. SERC, Daresbury Laboratory, Warrington, UK

  36. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Macromol Crystallogr A 276:307–326

    Article  CAS  Google Scholar 

  37. Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM (2008) MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics 9:403

    Article  PubMed Central  PubMed  Google Scholar 

  38. Perrakis A, Morris R, Lamzin VS (1999) Automated protein model building combined with iterative structure refinement. Nat Struct Biol 6(5):458–463

    Article  CAS  PubMed  Google Scholar 

  39. Pinkett HW, Lee AT, Lum P, Locher KP, Rees DC (2007) An inward-facing conformation of a putative metal-chelate-type ABC transporter. Science 315(5810):373–377

    Article  CAS  PubMed  Google Scholar 

  40. Reizer J, Reizer A, Saier MH Jr (1992) A new subfamily of bacterial ABC-type transport systems catalyzing export of drugs and carbohydrates. Protein Sci 1(10):1326–1332

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  41. Reyes CL, Chang G (2005) Structure of the ABC transporter MsbA in complex with ADP· vanadate and lipopolysaccharide. Science 308(5724):1028–1031

    Article  CAS  PubMed  Google Scholar 

  42. Rosenbaum G, Alkire RW, Evans G, Rotella FJ, Lazarski K, Zhang RG, Ginell SL, Duke N, Naday I, Lazarz J, Molitsky MJ, Keefe L, Gonczy J, Rock L, Sanishvili R, Walsh MA, Westbrook E, Joachimiak A (2006) The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results. J Synchrotron Radiat 13(Pt 1):30–45

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  43. Saier MH Jr, Paulsen IT, Sliwinski MK, Pao SS, Skurray RA, Nikaido H (1998) Evolutionary origins of multidrug and drug-specific efflux pumps in bacteria. Faseb J 12(3):265–274

    CAS  PubMed  Google Scholar 

  44. Schwede T, Kopp J, Guex N, Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 31(13):3381–3385

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  45. Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64(Pt 1):112–122

    Article  CAS  PubMed  Google Scholar 

  46. Smith PC, Karpowich N, Millen L, Moody JE, Rosen J, Thomas PJ, Hunt JF (2002) ATP binding to the motor domain from an ABC transporter drives formation of a nucleotide sandwich dimer. Mol Cell 10(1):139–149

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  47. Soding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21(7):951–960

    Article  PubMed  Google Scholar 

  48. Soding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33(Web Server issue):W244–W248

    Article  PubMed Central  PubMed  Google Scholar 

  49. Tam R, Saier MHJ (1993) A bacterial periplasmic receptor homologue with catalytic activity: cyclohexadienyl dehydratase of Pseudomonas aeruginosa is homologous to receptors specific for polar amino acids. Res Microbiol 144(3):165–169

    Article  CAS  PubMed  Google Scholar 

  50. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41

    Article  PubMed Central  PubMed  Google Scholar 

  51. Tusnady GE, Simon I (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics 17(9):849–850

    Article  CAS  PubMed  Google Scholar 

  52. Vakser IA (1997) Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex. Proteins 29(Suppl 1):226–230

    Article  Google Scholar 

  53. von Heijne G (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J Mol Biol 225(2):487–494

    Article  Google Scholar 

  54. Walker JE, Saraste M, Runswick MJ, Gay NJ (1982) Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1(8):945–951

    CAS  PubMed Central  PubMed  Google Scholar 

  55. Wallner B, Elofsson A (2007) Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins 69(Suppl 8):184–193

    Article  CAS  PubMed  Google Scholar 

  56. Wei Y, Guffanti AA, Krulwich TA (1999) Sequence analysis and functional studies of a chromosomal region of alkaliphilic Bacillus firmus OF4 encoding an ABC-type transporter with similarity of sequence and Na+ exclusion capacity to the Bacillus subtilis NatAB transporter. Extremophiles 3(2):113–120

    Article  CAS  PubMed  Google Scholar 

  57. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67(Pt 4):235–242

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  58. Yang H, Guranovic V, Dutta S, Feng Z, Berman HM, Westbrook JD (2004) Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr D Biol Crystallogr 60(Pt 10):1833–1839

    Article  PubMed  Google Scholar 

  59. Zaitseva J, Oswald C, Jumpertz T, Jenewein S, Wiedenmann A, Holland IB, Schmitt L (2006) A structural analysis of asymmetry required for catalytic activity of an ABC-ATPase domain dimer. EMBO J 25(14):3432–3443

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  60. Zhang CT, Zhang R (2001) A refined accuracy index to evaluate algorithms of protein secondary structure prediction. Proteins 43(4):520–522

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The work described in this paper was supported by NIH PSI Grants GM74492 and GM094585. The results shown in this report are derived from work performed at Argonne National Laboratory, at the Structural Biology Center of the Advanced Photon Source. Argonne is operated by University of Chicago Argonne, LLC, for the U.S. Department of Energy, Office of Biological and Environmental Research under contract DE-AC02-06CH11357. We would also like to thank Dr Matthew D. Zimmerman for critically reading and correcting the manuscript.

Author information

Author notes

  1. Ekaterina V. Filippova

    Present address: Department of Biochemistry and Molecular Genetics, Northwestern University, 303 E. Chicago Ave., Chicago, IL, 60611, USA

  2. Maksymilian Chruszcz

    Present address: Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA

Authors and Affiliations

  1. Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA

    Ekaterina V. Filippova, Karolina L. Tkaczuk, Maksymilian Chruszcz & Wladek Minor

  2. Midwest Center for Structural Genomics http://www.mcsg.anl.gov

    Ekaterina V. Filippova, Karolina L. Tkaczuk, Maksymilian Chruszcz, Xiaohui Xu, Alexei Savchenko, Aled Edwards & Wladek Minor

  3. Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, ON, M5G 1L6, Canada

    Xiaohui Xu, Alexei Savchenko & Aled Edwards

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  1. Ekaterina V. Filippova
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Correspondence to Wladek Minor.

Additional information

Ekaterina V. Filippova and Karolina L. Tkaczuk have contributed equally to the project.

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10969_2014_9189_MOESM1_ESM.tif

Multiple sequence alignment. Multiple sequence alignment (MSA) of the full-length sequence of TM0543 from Thermotoga maritima MSB8 and B subtilis NatB (GI 1663528). TM0543 homologs from other bacteria are Capnocytophaga sp. Oral, (326336280), Clostridium acetobutylicum (15896183), Thermotoga neapolitana (222099099), Thermatoga sp. (170288195), T. lettingae (157364685), and Dictyoglomus turgidum (217967947). TM0543 homologs from Archaea and Euryarchaeota are Thermococcus onnurineus (212224498), T. kodakarensis (57641271), Thermococcus sp. (254173813), T. gammatolerans (240103178), T. barophilus (315231269), T. sibiricus (242399363) Pyrococcus abyssi (14520847), P. horikoshii (14591313), and P. furiosus (18976681). Residues with > 70 % sequence similarity or identity are shaded gray; very highly conserved residues secondary structure elements are shown in cartoon representation above the MSA and colored according to the solution type (purple: experimentally solved, blue: modeled TM helices). The locations of the degenerate Walker A and Walker B nucleotide-binding motifs are marked in green above the alignment (TIFF 10425 kb)

10969_2014_9189_MOESM2_ESM.tif

Model structure of the transmembrane binding domain. Ribbon diagram of the putative NatAB-like ABC-type transporter TM0543 from Thermotoga maritima MSB8. The experimentally determined structure of ATP-BD is colored in purple, and the homology-modeled regions of TMD (and parts of ATP-BD) are colored in blue. ATP-BD helices are labeled as α and TMD helices are labeled as TM. (TM1 and TM2 are linker helices). The N- and C-termini are marked in red (TIFF 2890 kb)

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Filippova, E.V., Tkaczuk, K.L., Chruszcz, M. et al. Structural characterization of the putative ABC-type 2 transporter from Thermotoga maritima MSB8. J Struct Funct Genomics 15, 215–222 (2014). https://doi.org/10.1007/s10969-014-9189-7

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