Solution NMR and X-ray crystal structures of membrane-associated Lipoprotein-17 domain reveal a novel fold

  • Rajeswari Mani
  • Sergey Vorobiev
  • G. V. T. Swapna
  • Helen Neely
  • Haleema Janjua
  • Colleen Ciccosanti
  • Rong Xiao
  • Thomas B. Acton
  • John K. Everett
  • John Hunt
  • Gaetano T. Montelione
Article
  • 90 Downloads

Abstract

The conserved Lipoprotein-17 domain of membrane-associated protein Q9PRA0_UREPA from Ureaplasma parvum was selected for structure determination by the Northeast Structural Genomics Consortium, as part of the Protein Structure Initiative’s program on structure–function analysis of protein domains from large domain sequence families lacking structural representatives. The 100-residue Lipoprotein-17 domain is a “domain of unknown function” (DUF) that is a member of Pfam protein family PF04200, a large domain family for which no members have characterized biochemical functions. The three-dimensional structure of the Lipoprotein-17 domain of protein Q9PRA0_UREPA was determined by both solution NMR and by X-ray crystallography at 2.5 Å. The two structures are in good agreement with each other. The domain structure features three α-helices, α1 through α3, and five β-strands. Strands β1/β2, β3/β4, β4/β5 are anti-parallel to each other. Strands β1and β2 are orthogonal to strands β3, β4, β5, while helix α3 is formed between the strands β3 and β4. One-turn helix α2 is formed between the strands β1 and β2, while helix α1 occurs in the N-terminal polypeptide segment. Searches of the Protein Data Bank do not identify any other protein with significant structural similarity to Lipoprotein-17 domain of Q9PRA0_UREPA, indicating that it is a novel protein fold.

Keywords

Structural genomics Lipoprotein-17 domain of Q9PRA0_UREPA Domains of unknown function (DUFs) Lipoprotein Ureaplasma parvum Northeast Structural Genomics Consortium (NESG) Solution NMR X-ray crystal structure 

Notes

Acknowledgments

We thank Prof. M. Inouye for advice regarding the biology and biochemistry of bacterial lipoproteins. This work was supported by a grant from the Protein Structure Initiative of National Institute of General Medical Sciences, U54-GM074958. NMR (2KRT) and X-ray structures [3JVC (2.7 Å resolution); 3K63 (2.5 Å resolution)] of the Lipoprotein-17 domain have been submitted to the Protein Data Bank. Chemical shifts, NMR constraints, NOESY FID data, and NOESY peak list data have been deposited in the BioMagResDatabase (16648). Expression plasmids for Lipoprotein-17 domain of Q9PRA0_UREPA are available from the PSI Materials Repository (http://psimr.asu.edu/).

Supplementary material

10969_2010_9099_MOESM1_ESM.doc (578 kb)
Supplementary material 1 (DOC 578 kb)

References

  1. 1.
    Acton TB, Gunsalus KC, Xiao R, Ma LC, Aramini J, Baran MC, Chiang YW, 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 394:210–243PubMedCrossRefGoogle Scholar
  2. 2.
    Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58:1948–1954PubMedCrossRefGoogle Scholar
  3. 3.
    Baran MC, Huang YJ, Moseley HN, Montelione GT (2004) Automated analysis of protein NMR assignments and structures. Chem Rev 104:3541–3556PubMedCrossRefGoogle Scholar
  4. 4.
    Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL (2002) The Pfam protein families database. Nucleic Acids Res 30:276–280PubMedCrossRefGoogle Scholar
  5. 5.
    Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66:778–795PubMedCrossRefGoogle Scholar
  6. 6.
    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 & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D 54:905–921PubMedCrossRefGoogle Scholar
  7. 7.
    Chayen NE, Stewart PDS, Maeder DL, Blow DM (1990) An automated system for micro-batch protein crystallization and screening. J Appl Cryst 23:297–302CrossRefGoogle Scholar
  8. 8.
    DeLano WL (2002) The pymol manual. DeLano Scientific, San CarlosGoogle Scholar
  9. 9.
    Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132PubMedCrossRefGoogle Scholar
  10. 10.
    Glass JI, Lefkowitz EJ, Glass JS, Heiner CR, Chen EY, Cassell GH (2000) The complete sequence of the mucosal pathogen Ureaplasma urealyticum. Nature 407:757–762PubMedCrossRefGoogle Scholar
  11. 11.
    Guntert P, Mumenthaler C, Wuthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273:283–298PubMedCrossRefGoogle Scholar
  12. 12.
    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 319:209–227PubMedCrossRefGoogle Scholar
  13. 13.
    Holm L, Sander C (1995) Dali: a network tool for protein structure comparison. Trends Biochem Sci 20:478–480PubMedCrossRefGoogle Scholar
  14. 14.
    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 127:1665–1674PubMedCrossRefGoogle Scholar
  15. 15.
    Huang YJ, Tejero R, Powers R, Montelione GT (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data. Proteins 62:587–603PubMedCrossRefGoogle Scholar
  16. 16.
    Koradi R, Billeter M, Wuthrich K (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14:29–32CrossRefGoogle Scholar
  17. 17.
    Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993) Procheck—a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291CrossRefGoogle Scholar
  18. 18.
    Linge JP, Williams MA, Spronk CA, Bonvin AM, Nilges M (2003) Refinement of protein structures in explicit solvent. Proteins 50:496–506PubMedCrossRefGoogle Scholar
  19. 19.
    Liu GH, 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 102:10487–10492PubMedCrossRefGoogle Scholar
  20. 20.
    Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307–326CrossRefGoogle Scholar
  21. 21.
    Schneider TR, Sheldrick GM (2002) Substructure solution with SHELXD. Acta Crystallogr D Biol Crystallogr 58:1772–1779PubMedCrossRefGoogle Scholar
  22. 22.
    Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS + : a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213–223PubMedCrossRefGoogle Scholar
  23. 23.
    Terwilliger TC (2003) SOLVE and RESOLVE: automated structure solution and density modification. Methods Enzymol 374:22–37PubMedCrossRefGoogle Scholar
  24. 24.
    Wishart DS, Sykes BD (1994) The C-13 Chemical-Shift Index—a simple method for the identification of protein secondary structure using C-13 chemical-shift data. J Biomol NMR 4:171–180PubMedCrossRefGoogle Scholar
  25. 25.
    Word JM, Bateman RC, Presley BK, Lovell SC, Richardson DC (2000) Exploring steric constraints on protein mutations using MAGE/PROBE. Protein Sci 9:2251–2259PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Rajeswari Mani
    • 1
  • Sergey Vorobiev
    • 2
  • G. V. T. Swapna
    • 1
  • Helen Neely
    • 2
  • Haleema Janjua
    • 1
  • Colleen Ciccosanti
    • 1
  • Rong Xiao
    • 1
  • Thomas B. Acton
    • 1
  • John K. Everett
    • 1
  • John Hunt
    • 2
  • Gaetano T. Montelione
    • 1
    • 3
  1. 1.Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium (NESG)Rutgers, The State University of New JerseyPiscatawayUSA
  2. 2.Department of Biological Sciences, Northeast Structural Genomics ConsortiumColumbia UniversityNew YorkUSA
  3. 3.Robert Wood Johnson Medical SchoolUniversity of Medicine and Dentistry of New JerseyPiscatawayUSA

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