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Solution NMR structure of CD1104B from pathogenic Clostridium difficile reveals a distinct α-helical architecture and provides first structural representative of protein domain family PF14203

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Journal of Structural and Functional Genomics

Abstract

A high-quality structure of the 68-residue protein CD1104B from Clostridium difficile strain 630 exhibits a distinct all α-helical fold. The structure presented here is the first representative of bacterial protein domain family PF14203 (currently 180 members) of unknown function (DUF4319) and reveals that the side-chains of the only two strictly conserved residues (Glu 8 and Lys 48) form a salt bridge. Moreover, these two residues are located in the vicinity of the largest surface cleft which is predicted to contribute to a surface area involved in protein–protein interactions. This, along with its coding in transposon CTn4, suggests that CD1104B (and very likely all members of Pfam 14203) functions by interacting with other proteins required for the transfer of transposons between different bacterial species.

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Fig. 1

Abbreviations

ABC:

ATP-binding cassette

CD:

Clostridium difficile

CTn:

Conjugative transposon

DSS:

4,4-dimethyl-4-silapentane-1-sulfonate sodium salt

DTT:

Dithiothreitol

DUF:

Domain of unknown function

MES:

2-(N-morpholino)ethanesulfonic acid

NESG:

Northeast Structural Genomics Consortium

NOE:

Nuclear overhauser effect

PDB:

Protein data bank

RDC:

Residual dipolar coupling

RMSD:

Root mean square deviation

References

  1. He M, Miyajima F, Roberts P, Ellison L, Pickard DJ, Martin MJ, Connor TR, Harris SR, Fairley D, Bamford KB, D’Arc S, Brazier J, Brown D, Coia JE, Douce G, Gerding D, Kim HJ, Koh TH, Kato H, Senoh M, Louie T, Michell S, Butt E, Peacock SJ, Brown NM, Riley T, Songer G, Wilcox M, Pirmohamed M, Kuijper E, Hawkey P, Wren BW, Dougan G, Parkhill J, Lawley TD (2013) Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat Genet 45:109–113

    Article  PubMed  CAS  Google Scholar 

  2. Brouwer MSM, Warburton PJ, Roberts AP, Mullany P, Allan E (2011) Genetic organisation, mobility and predicted functions of genes on integrated, mobile genetic elements in sequenced strains of Clostridium difficile. PLoS ONE 6:e23014

    Article  PubMed  CAS  Google Scholar 

  3. Sebaihia M, Wren BW, Mullany P, Fairweather NF, Minton N, Stabler R, Thomson NR, Roberts AP, Cerdeno-Tarraga AM, Wang H, Holden MTG, Wright A, Churcher C, Quail MA, Baker S, Bason N, Brooks K, Chillingworth T, Cronin A, Davis P, Dowd L, Fraser A, Feltwell T, Hance Z, Holroyd S, Jagels K, Moule S, Mungall K, Price C, Rabbinowitsch E, Sharp S, Simmonds M, Stevens K, Unwin L, Whithead S, Dupuy B, Dougan G, Barrell B, Parkhill J (2006) The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet 38:779–786

    Article  PubMed  Google Scholar 

  4. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer ELL, Eddy SR, Bateman A (2010) The Pfam protein families database. Nucleic Acids Res 38:D211–D222

    Article  PubMed  CAS  Google Scholar 

  5. Dessailly BH, Nair R, Jaroszewski L, Fajardo JE, Kouranov A, Lee D, Fiser A, Godzik A, Rost B, Orengo C (2009) PSI-2: structural genomics to cover protein domain family space. Structure 17:869–881

    Article  PubMed  CAS  Google Scholar 

  6. Liu JF, Montelione GT, Rost B (2007) Novel leverage of structural genomics. Nat Biotechnol 25:850–853

    Google Scholar 

  7. Acton TB, Gunsalus KC, Xiao R, Ma LC, Aramini J, Baran MC, Chiang Y-W, Climent T, Cooper B, Denissova NG, Douglas SM, Everett JK, Ho CK, Macapagal D, Rajan PK, Shastry R, Shih LY, Swapna GVT, Wilson M, Wu M, Gerstein M, Inouye M, Hunt JF, Montelione GT (2005) Robotic cloning and protein production platform of the Northeast Structural Genomics Consortium. Methods Enzymol 394:210–243

    Article  PubMed  CAS  Google Scholar 

  8. Acton TB, Xiao R, Anderson S, Aramini J, Buchwald WA, Ciccosanti C, Conover K, Everett J, Hamilton K, Huang YJ, Janjua H, Kornhaber G, Lau J, Lee DY, Liu GH, Maglaqui M, Ma LC, Mao L, Patel D, Rossi P, Sahdev S, Shastry R, Swapna GVT, Tang YF, Tong SC, Wang DY, Wang H, Zhao L, Montelione GT (2011) Preparation of protein samples for NMR structure, function, and small-molecule screening studies. Fragment-based drug design: tools, practical approaches, and examples. Methods Enzymol 493:21–60

    Google Scholar 

  9. Xiao R, Anderson S, Aramini J, Belote R, Buchwald WA, Ciccosanti C, Conover K, Everett JK, Hamilton K, Huang YJ, Janjua H, Jiang M, Kornhaber GJ, Lee DY, Locke JY, Ma L-C, Maglaqui M, Mao L, Mitra S, Patel D, Rossi P, Sahdev S, Sharma S, Shastry R, Swapna GVT, Tong SN, Wang D, Wang H, Zhao L, Montelione GT, Acton TB (2010) The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium. J Struct Biol 172:21–33

    Article  PubMed  CAS  Google Scholar 

  10. Neri D, Szyperski T, Otting G, Senn H, Wuthrich K (1989) Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling. Biochemistry 28:7510–7516

    Article  PubMed  CAS  Google Scholar 

  11. Kim S, Szyperski T (2003) GFT NMR, a new approach to rapidly obtain precise high-dimensional NMR spectral information. J Am Chem Soc 125:1385–1393

    Article  PubMed  CAS  Google Scholar 

  12. Moseley HNB, Monleon D, Montelione GT (2001) Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Nuclear Magnetic Resonance of Biological Macromolecules, Pt B. Methods Enzymol 339:91–108

    Google Scholar 

  13. Zimmerman DE, Kulikowski CA, Huang YP, Feng WQ, Tashiro M, Shimotakahara S, Chien CY, Powers R, Montelione GT (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol 269:592–610

    Article  PubMed  CAS  Google Scholar 

  14. Moseley HNB, Sahota G, Montelione GT (2004) Assignment validation software suite for the evaluation and presentation of protein resonance assignment data. J Biomol NMR 28:341–355

    Article  PubMed  CAS  Google Scholar 

  15. Huang YJ, Powers R, Montelione GT (2005) Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 127:1665–1674

    Article  PubMed  CAS  Google Scholar 

  16. Liu G, Shen Y, Atreya HS, Parish D, Shao Y, Sukumaran DK, Xiao R, Yee A, Lemak A, Bhattacharya A, Acton TA, Arrowsmith CH, Montelione GT, Szyperski T (2005) NMR data collection and analysis protocol for high-throughput protein structure determination. Proc Natl Acad Sci USA 102:10487–10492

    Article  PubMed  CAS  Google Scholar 

  17. Guntert P, Mumenthaler C, Wuthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273:283–298

    Article  PubMed  CAS  Google Scholar 

  18. Herrmann T, Guntert P, Wuthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209–227

    Article  PubMed  CAS  Google Scholar 

  19. Huang YJ, Tejero R, Powers R, Montelione GT (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data. Proteins 62:587–603

    Article  PubMed  CAS  Google Scholar 

  20. Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289–302

    Article  PubMed  CAS  Google Scholar 

  21. Liu Y, Prestegard JH (2009) Measurement of one and two bond N–C couplings in large proteins by TROSY-based J-modulation experiments. J Magn Reson 200:109–118

    Article  PubMed  CAS  Google Scholar 

  22. Linge JP, Williams MA, Spronk C, Bonvin A, Nilges M (2003) Refinement of protein structures in explicit solvent. Proteins 50:496–506

    Article  PubMed  CAS  Google Scholar 

  23. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr Sect D Biol Crystallogr 54:905–921

    Article  CAS  Google Scholar 

  24. Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66:778–795

    Article  PubMed  CAS  Google Scholar 

  25. Altschul SF, Madden TL, Schäffer 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 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  26. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235–242

    Article  PubMed  CAS  Google Scholar 

  27. Holm L, Sander C (1995) Dali: a network tool for protein structure comparison. Trends Biochem Sci 20:478–480

    Article  PubMed  CAS  Google Scholar 

  28. Nayal M, Honig B (2006) On the nature of cavities on protein surfaces: application to the identification of drug-binding sites. Proteins 63:892–906

    Article  PubMed  CAS  Google Scholar 

  29. Petrey D, Fischer M, Honig B (2009) Structural relationships among proteins with different global topologies and their implications for function annotation strategies. Proc Natl Acad Sci U S A 106:17377–17382

    Article  PubMed  CAS  Google Scholar 

  30. Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res 38:W529–W533

    Article  PubMed  CAS  Google Scholar 

  31. Xu D, Tsai CJ, Nussinov R (1997) Hydrogen bonds and salt bridges across protein–protein interfaces. Protein Eng 10:999–1012

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  33. Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D (2011) PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res 39:W283–W287

    Article  PubMed  CAS  Google Scholar 

  34. Zhang QC, Petrey D, Norel R, Honig BH (2010) Protein interface conservation across structure space. Proc Natl Acad Sci U S A 107:10896–10901

    Article  PubMed  CAS  Google Scholar 

  35. Nair R, Liu J, Soong T–T, Acton TB, Everett JK, Kouranov A, Fiser A, Godzik A, Jaroszewski L, Orengo C, Montelione GT, Rost B (2009) Structural genomics is the largest contributor of novel structural leverage. J Struct Funct Genomics 10:181–191

    Article  PubMed  CAS  Google Scholar 

  36. Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66:778–795

    Article  PubMed  CAS  Google Scholar 

  37. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539

    Google Scholar 

  38. Gouet P, Robert X, Courcelle E (2003) ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res 31:3320–3323

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

This work was supported by the National Institutes of Health, Grant Number: U54 GM094597 (T.S., J.H.P. and G.T.M.).

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Author notes

  1. Hsiau-Wei Lee

    Present address: Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA, 95064, USA

Authors and Affiliations

  1. Department of Chemistry, The State University of New York at Buffalo and Northeast Structural Genomics Consortium, Buffalo, NY, 14260, USA

    Surya V. S. R. K. Pulavarti, Alexander Eletsky & Thomas Szyperski

  2. Complex Carbohydrate Research Center, University at Georgia and Northeast Structural Genomics Consortium, Athens, GA, 30602, USA

    Hsiau-Wei Lee & James H. Prestegard

  3. Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ, 08854, USA

    Thomas B. Acton, Rong Xiao & John K. Everett

  4. Department of Biochemistry and Molecular Biology Robert Wood Johnson Medical School, UMDNJ, Piscataway, NJ, 08854, USA

    Gaetano T. Montelione

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Pulavarti, S.V.S.R.K., Eletsky, A., Lee, HW. et al. Solution NMR structure of CD1104B from pathogenic Clostridium difficile reveals a distinct α-helical architecture and provides first structural representative of protein domain family PF14203. J Struct Funct Genomics 14, 155–160 (2013). https://doi.org/10.1007/s10969-013-9164-8

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