Solution NMR and X-ray crystal structures of Pseudomonas syringae Pspto_3016 from protein domain family PF04237 (DUF419) adopt a “double wing” DNA binding motif

Journal of Structural and Functional Genomics - Tập 13 - Trang 155-162 - 2012
Erik A. Feldmann1,2, Jayaraman Seetharaman2,3, Theresa A. Ramelot1,2, Scott Lew2,3, Li Zhao4, Keith Hamilton2,4, Colleen Ciccosanti2,4, Rong Xiao2,4, Thomas B. Acton2,4, John K. Everett2,4, Liang Tong2,3, Gaetano T. Montelione2,4,5, Michael A. Kennedy1,2
1Department of Chemistry and Biochemistry, Miami University, Oxford, USA
2Northeast Structural Genomics Consortium, Piscataway, USA
3Department of Biological Sciences, Columbia University, New York, USA
4Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, USA
5Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, USA

Tóm tắt

The protein Pspto_3016 is a 117-residue member of the protein domain family PF04237 (DUF419), which is to date a functionally uncharacterized family of proteins. In this report, we describe the structure of Pspto_3016 from Pseudomonas syringae solved by both solution NMR and X-ray crystallography at 2.5 Å resolution. In both cases, the structure of Pspto_3016 adopts a “double wing” α/β sandwich fold similar to that of protein YjbR from Escherichia coli and to the C-terminal DNA binding domain of the MotA transcription factor (MotCF) from T4 bacteriophage, along with other uncharacterized proteins. Pspto_3016 was selected by the Protein Structure Initiative of the National Institutes of Health and the Northeast Structural Genomics Consortium (NESG ID PsR293).

Tài liệu tham khảo

Acton TB, Xiao R, Anderson S, Aramini J, Buchwald W, Ciccosanti C, Conover K, Everett JK, Hamilton K, Huang Y, Janjua H, Kornhaber G, Lau J, Lee D, Liu G, Maglaqui M, Ma L, Mao L, Patel D, Rossi P, Sahdev S, Shastry R, Swapna GVT, Tang Y, Tong S, Wang D, Wang H, Zhao L, Montelione GT (2010) Preparation of protein samples for NMR structure, function, and small-molecule screening studies. Methods Enzymol 493:21–60 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 Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98:10037–10041 Battacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consotria. Proteins 66:778–795 Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453–1462 Brünger 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 Biol Crystallogr 54:905–921 Buell CR, Joardar V, Lindeberg M, Selengut J, Paulsen IT, Gwinn ML, Dodson RJ, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Daugherty S, Brinkac L, Beanan MJ, Haft DH, Nelson WC, Davidsen T, Zafar N, Zhou L, Liu J, Yuan Q, Khouri H, Fedorova N, Tran B, Russell D, Berry K, Utterback T, Van Aken SE, Feldblyum TV, D’Ascenzo M, Deng WL, Ramos AR, Alfano JR, Cartinhour S, Chatterjee AK, Delaney TP, Lazarowitz SG, Martin GB, Schneider DJ, Tang X, Bender CL, White O, Fraser CM, Collmer A (2003) The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci USA 100:10181–10186 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 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 Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132 Finnin MS, Cicero MP, Davies C, Porter SJ, White SW, Kreuzer KN (1997) The activation domain of the MotA transcription factor from bacteriophage T4. EMBO J 16:1992–2003 Finnin MS, Hoffman DW, White SW (1994) The DNA-binding domain of the MotA transcription factor from bacteriophage T4 shows structural similarity to the TATA-binding protein. Proc Natl Acad Sci USA 91:10972–10976 Frickey T, Lupas A (2004) CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics 20:3702–3704 Gabanyi MJ, Adams PD, Arnold K, Bordoli L, Carter LG, Flippen-Andersen J, Gifford L, Haas J, Kouranov A, McLaughlin WA, Micallef DI, Minor W, Shah R, Schwede T, Tao YP, Westbrook JD, Zimmerman M, Berman HM (2011) The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J Struct Funct Genomics 12:45–54 Güntert P (2004) Automated NMR structure calculation with CYANA. Methods Mol Biol 278:353–378 Herrmann T, Güntert P, Wüthrich 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 Holm L, Rosenström P (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38:W545–W549 Huang YJ, Moseley HN, Baran MC, Arrowsmith C, Powers R, Tejero R, Szyperski T, Montelione GT (2005) An integrated platform for automated analysis of protein NMR structures. Methods Enzymol 394:111–141 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 Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30 Li N, Sickmier EA, Zhang R, Joachimiak A, White SW (2002) The MotA transcription factor from bacteriophage T4 contains a novel DNA-binding domain: the ‘double wing’ motif. Mol Microbiol 43:1079–1088 Li N, Zhang W, White SW, Kriwacki RW (2001) Solution structure of the transcriptional activation domain of the bacteriophage T4 protein, MotA. Biochemistry 40:4293–4302 Liu J, Montelione GT, Rost B (2007) Novel leverage of structural genomics. Nat Biotechnol 25:849–851 Moseley HN, Monleon D, Montelione GT (2001) Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Methods Enzymol 339:91–108 Otwinowski Z, Minor W (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode. Methods Enzymol 276:307–326 Perrakis A, Morris R, Lamzin VS (1999) Automated protein model building combined with iterative structure refinement. Nat Struct Biol 6:458–463 Schrödinger L (2002) The PyMOL Molecular Graphics System, Version 0.99rc6 Schwieters C, Kuszewski J, Clore G (2006) Using Xplor-NIH for NMR molecular structure determination. Prog Nucl Mag Res Spectrosc 48:47–62 Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64:112–122 Singarapu KK, Liu G, Xiao R, Bertonati C, Honig B, Montelione GT, Szyperski T (2007) NMR structure of protein yjbR from Escherichia coli reveals ‘double-wing’ DNA binding motif. Proteins 67:501–504 Terwilliger TC (2003) Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr D Biol Crystallogr 59:38–44 Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680