Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771

  • Alexander Eletsky
  • Donald Petrey
  • Qiangfeng Cliff Zhang
  • Hsiau-Wei Lee
  • Thomas B. Acton
  • Rong Xiao
  • John K. Everett
  • James H. Prestegard
  • Barry Honig
  • Gaetano T. Montelione
  • Thomas Szyperski


High-quality NMR structures of the homo-dimeric proteins Bvu3908 (69-residues in monomeric unit) from Bacteroides vulgatus and Bt2368 (74-residues) from Bacteroides thetaiotaomicron reveal the presence of winged helix-turn-helix (wHTH) motifs mediating tight complex formation. Such homo-dimer formation by winged HTH motifs is otherwise found only in two DNA-binding proteins with known structure: the C-terminal wHTH domain of transcriptional activator FadR from E. coli and protein TubR from B. thurigensis, which is involved in plasmid DNA segregation. However, the relative orientation of the wHTH motifs is different and residues involved in DNA-binding are not conserved in Bvu3908 and Bt2368. Hence, the proteins of the present study are not very likely to bind DNA, but are likely to exhibit a function that has thus far not been ascribed to homo-dimers formed by winged HTH motifs. The structures of Bvu3908 and Bt2368 are the first atomic resolution structures for PFAM family PF10771, a family of unknown function (DUF2582) currently containing 128 members.


Bvu3908 Bt2368 PF10771 DUF2582 Winged helix-turn-helix Structural genomics 



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






2-(N-Morpholino)ethanesulfonic acid


Northeast Structural Genomics Consortium


Nuclear Overhauser effect


Protein Data Bank


Residual dipolar coupling


Root mean square deviation


Winged helix-turn-helix



We thank D. Wang, C. Ciccosanti, K. Hamilton and S. Bhattacharya for helpful discussions and technical support. This work was supported by the National Institutes of Health, grant number: U54 GM094597 (T.S. and G.T.M.). While data acquisition was in progress, Prof. T. Szyperski was a member of the New York Structural Biology Center. The Center is a STAR center supported by the New York State Office of Science, Technology, and Academic Research.

Supplementary material

10969_2011_9121_MOESM1_ESM.doc (5.3 mb)
Supplementary material 1 (DOC 5,411 kb)


  1. 1.
    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–D222PubMedCrossRefGoogle Scholar
  2. 2.
    Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, Hooper LV, Gordon JI (2003) A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 299:2074–2076PubMedCrossRefGoogle Scholar
  3. 3.
    Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton RS, Fulton LA, Clifton SW, Wilson RK, Knight RD, Gordon JI (2007) Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 5:1574–1586Google Scholar
  4. 4.
    Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE (2006) Metagenomic analysis of the human distal gut microbiome. Science 312:1355–1359PubMedCrossRefGoogle Scholar
  5. 5.
    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) Nuclear magnetic resonance of biological macromolecules, Part C. In: James TL (ed) Methods in enzymology, vol 394. Elsevier, San Diego, pp 210–243Google Scholar
  6. 6.
    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 LC, Maglaqui M, Mao L, Mitra S, Patel D, Rossi P, Sahdev S, Sharma S, Shastry R, Swapna GVT, Tong SN, Wang DY, Wang HA, Zhao L, Montelione GT, Acton TB (2010) The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium. J Struct Biol 172:21–33PubMedCrossRefGoogle Scholar
  7. 7.
    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) Fragment-based drug design: tools, practical approaches, and examples. In: Kuo LC (ed) Methods in enzymology, vol 493. Elsevier, San Diego, pp 21–60Google Scholar
  8. 8.
    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 28:7510–7516PubMedCrossRefGoogle Scholar
  9. 9.
    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 269:592–610PubMedCrossRefGoogle Scholar
  10. 10.
    Moseley HNB, Monleon D, Montelione GT (2001) Nuclear magnetic resonance of biological macromolecules, Pt B. In: James TL, Dötsch V, Schmitz U (eds) Methods in enzymology, vol 339. Elsevier, San Diego, pp 91–108Google Scholar
  11. 11.
    Moseley HNB, Sahota G, Montelione GT (2004) Assignment validation software suite for the evaluation and presentation of protein resonance assignment data. J Biomol NMR 28:341–355PubMedCrossRefGoogle Scholar
  12. 12.
    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
  13. 13.
    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
  14. 14.
    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
  15. 15.
    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
  16. 16.
    Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289–302PubMedCrossRefGoogle Scholar
  17. 17.
    Linge JP, Williams MA, Spronk C, Bonvin A, Nilges M (2003) Refinement of protein structures in explicit solvent. Proteins 50:496–506PubMedCrossRefGoogle Scholar
  18. 18.
    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 Sect D Biol Crystallogr 54:905–921CrossRefGoogle Scholar
  19. 19.
    Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins Struct Funct Bioinf 66:778–795CrossRefGoogle Scholar
  20. 20.
    Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedCrossRefGoogle Scholar
  21. 21.
    Liu JF, Montelione GT, Rost B (2007) Novel leverage of structural genomics. Nat Biotechnol 25:850–853Google Scholar
  22. 22.
    Petrey D, Honig B (2003) Macromolecular crystallography, Pt D. In: Carter CW, Sweet RM (eds) Methods in enzymology, vol 374. Elsevier, San Diego, pp 492–509Google Scholar
  23. 23.
    Yang AS, Honig B (2000) An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance. J Mol Biol 301:665–678PubMedCrossRefGoogle Scholar
  24. 24.
    Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242PubMedCrossRefGoogle Scholar
  25. 25.
    Aravind L, Anantharaman V, Balaji S, Babu MM, Iyer LM (2005) The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiol Rev 29:231–262PubMedGoogle Scholar
  26. 26.
    Gajiwala KS, Burley SK (2000) Winged helix proteins. Curr Opin Struct Biol 10:110–116PubMedCrossRefGoogle Scholar
  27. 27.
    Laskowski RA, Watson JD, Thornton JM (2005) ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 33:W89–W93PubMedCrossRefGoogle Scholar
  28. 28.
    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 USA 106:17377–17382PubMedCrossRefGoogle Scholar
  29. 29.
    Holm L, Sander C (1995) Dali—a network tool for protein structure comparison. Trends Biochem Sci 20:478–480PubMedCrossRefGoogle Scholar
  30. 30.
    van Aalten DMF, Dirusso CC, Knudsen J (2001) The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR. EMBO J 20:2041–2050PubMedCrossRefGoogle Scholar
  31. 31.
    Xu YB, Heath RJ, Li ZM, Rock CO, White SW (2001) The FadR DNA complex—transcriptional control of fatty acid metabolism in Escherichia coli. J Biol Chem 276:17373–17379PubMedCrossRefGoogle Scholar
  32. 32.
    Ni LS, Xu WJ, Kumaraswami M, Schumacher MA (2010) Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition. Proc Natl Acad Sci USA 107:11763–11768PubMedCrossRefGoogle Scholar
  33. 33.
    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 10:181–191PubMedCrossRefGoogle Scholar
  34. 34.
    Laskowski RA, Rullmann JAC, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8:477–486PubMedCrossRefGoogle Scholar
  35. 35.
    Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr Sect D Biol Crystallogr 66:12–21CrossRefGoogle Scholar
  36. 36.
    Luthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with 3-dimensional profiles. Nature 356:83–85PubMedCrossRefGoogle Scholar
  37. 37.
    Sippl MJ (1993) Recognition of errors in 3-dimensional structures of proteins. Proteins 17:355–362PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Alexander Eletsky
    • 1
  • Donald Petrey
    • 2
  • Qiangfeng Cliff Zhang
    • 2
  • Hsiau-Wei Lee
    • 3
  • Thomas B. Acton
    • 4
    • 5
  • Rong Xiao
    • 4
    • 5
  • John K. Everett
    • 4
    • 5
  • James H. Prestegard
    • 3
  • Barry Honig
    • 2
  • Gaetano T. Montelione
    • 4
    • 5
  • Thomas Szyperski
    • 1
  1. 1.Department of ChemistryThe State University of New York at Buffalo, and Northeast Structural Genomics ConsortiumBuffaloUSA
  2. 2.Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Center for Computational Biology and BioinformaticsColumbia UniversityNew YorkUSA
  3. 3.Complex Carbohydrate Research CenterUniversity of Georgia, and Northeast Structural Genomics ConsortiumAthensUSA
  4. 4.Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and MedicineRutgers, The State University of New JerseyPiscatawayUSA
  5. 5.Department of Biochemistry, Robert Wood Johnson Medical SchoolUMDNJ, and Northeast Structural Genomics ConsortiumPiscatawayUSA

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