Journal of Biomolecular NMR

, Volume 60, Issue 2–3, pp 197–202 | Cite as

Solution structure of a C-terminal fragment (175–257) of CV_0373 protein from Chromobacterium violaceum adopts a winged helix-turn-helix (wHTH) fold

  • Yunhuang Yang
  • Theresa A. Ramelot
  • Hsiau-Wei Lee
  • Rong Xiao
  • John K. Everett
  • Gaetano T. Montelione
  • James H. Prestegard
  • Michael A. Kennedy
NMR structure note

References

  1. 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 G, Maglaqui M, Ma L, Mao L, Patel D, Rossi P, Sahdev S, Shastry R, Swapna GV, Tang Y, Tong S, Wang D, Wang H, Zhao L, Montelione GT (2011) Preparation of protein samples for NMR structure, function, and small-molecule screening studies. Methods Enzymol 493:21–60CrossRefGoogle Scholar
  2. Anantharaman V, Aravind L (2006) The NYN domains: novel predicted RNAses with a PIN domain-like fold. RNA Biol 3:18–27CrossRefGoogle Scholar
  3. Anantharaman V, Zhang D, Aravind L (2010) OST–HTH: a novel predicted RNA-binding domain. Biol Direct 5:13CrossRefGoogle Scholar
  4. 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–W533CrossRefGoogle Scholar
  5. Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66:778–795CrossRefGoogle Scholar
  6. Brazilian National Genome Project C (2003) The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability. Proc Natl Acad Sci USA 100:11660–11665CrossRefADSGoogle Scholar
  7. Cai ML, Huang Y, Suh JY, Louis JM, Ghirlando R, Craigie R, Clore GM (2007) Solution NMR structure of the barrier-to-autointegration factor-emerin complex. J Biol Chem 282:14525–14535CrossRefGoogle Scholar
  8. Callebaut I, Mornon JP (2010) LOTUS, a new domain associated with small RNA pathways in the germline. Bioinformatics 26:1140–1144CrossRefGoogle Scholar
  9. Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19:163–164CrossRefGoogle Scholar
  10. Guntert P (2004) Automated NMR structure calculation with CYANA. Methods Mol Biol 278:353–378Google Scholar
  11. Hansen MR, Mueller L, Pardi A (1998) Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nat Struct Biol 5:1065–1074CrossRefGoogle Scholar
  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 127:1665–1674CrossRefGoogle Scholar
  13. Kay LE, Torchia DA, Bax A (1989) Backbone dynamics of proteins as studied by 15 N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. Biochemistry 28:8972–8979CrossRefGoogle Scholar
  14. Kodach LL, Bos CL, Duran N, Peppelenbosch MP, Ferreira CV, Hardwick JC (2006) Violacein synergistically increases 5-fluorouracil cytotoxicity, induces apoptosis and inhibits Akt-mediated signal transduction in human colorectal cancer cells. Carcinogenesis 27:508–516CrossRefGoogle Scholar
  15. 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 28:7510–7516CrossRefGoogle Scholar
  16. Ruckert M, Otting G (2000) Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments. J Am Chem Soc 122:7793–7797CrossRefGoogle Scholar
  17. Schwieters CD, Kuszewski JJ, Clore GM (2006) Using Xplor-NIH for NMR molecular structure determination. Prog Nucl Magn Reson Spectrosc 48:47–62CrossRefGoogle Scholar
  18. Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS plus: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213–223CrossRefGoogle Scholar
  19. Tjandra N, Grzesiek S, Bax A (1996) Magnetic field dependence of nitrogen-proton J splittings in N-15-enriched human ubiquitin resulting from relaxation interference and residual dipolar coupling. J Am Chem Soc 118:6264–6272CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Yunhuang Yang
    • 1
  • Theresa A. Ramelot
    • 1
  • Hsiau-Wei Lee
    • 2
  • Rong Xiao
    • 3
  • John K. Everett
    • 3
  • Gaetano T. Montelione
    • 3
    • 4
  • James H. Prestegard
    • 2
  • Michael A. Kennedy
    • 1
  1. 1.Department of Chemistry and Biochemistry, and the Northeast Structural Genomics ConsortiumMiami UniversityOxfordUSA
  2. 2.Complex Carbohydrate Research Center, and the Northeast Structural Genomics ConsortiumUniversity of GeorgiaAthensUSA
  3. 3.Department of Molecular Biology and Biochemistry, and the Northeast Structural Genomics Consortium, Center for Advanced Biotechnology and MedicineRutgers, The State University of New JerseyPiscatawayUSA
  4. 4.Department of Biochemistry, Robert Wood Johnson Medical SchoolUniversity of Medicine and Dentistry of New JerseyPiscatawayUSA

Personalised recommendations