The crystal structure of pyrimidine/thiamin biosynthesis precursor-like domain-containing protein CAE31940 from proteobacterium Bordetella bronchiseptica RB50, and evolutionary insight into the NMT1/THI5 family

Journal of Structural and Functional Genomics - Tập 15 - Trang 73-81 - 2014
Jacek Bajor1,2, Karolina L. Tkaczuk1,2, Maksymilian Chruszcz1,2,3, Hutton Chapman1,2, Olga Kagan4,2, Alexei Savchenko4,2, Wladek Minor1,2
1Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
2Midwest Center for Structural Genomics, USA
3Department of Chemistry and Biochemistry, University of South Carolina, Columbia, USA
4Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada

Tóm tắt

We report a 2.0 Å structure of the CAE31940 protein, a proteobacterial NMT1/THI5-like domain-containing protein. We also discuss the primary and tertiary structure similarity with its homologs. The highly conserved FGGXMP motif was identified in CAE31940, which corresponds to the GCCCX motif located in the vicinity of the active center characteristic for THi5-like proteins found in yeast. This suggests that the FGGXMP motif may be a unique hallmark of proteobacterial NMT1/THI5-like proteins.

Tài liệu tham khảo

Zurlinden A, Schweingruber ME (1994) Cloning, nucleotide sequence, and regulation of Schizosaccharomyces pombe thi4, a thiamine biosynthetic gene. J Bacteriol 176:6631–6635 Begley TP, Chatterjee A, Hanes JW, Hazra A, Ealick SE (2008) Cofactor biosynthesis–still yielding fascinating new biological chemistry. Curr Opin Chem Biol 12(2):118–125 Bale S, Rajashankar KR, Perry K, Begley TP, Ealick SE (2010) HMP binding protein ThiY and HMP-P synthase THI5 are structural homologues. Biochemistry 49(41):8929–8936 Maundrell K (1990) nmt1 of fission yeast. A highly transcribed gene completely repressed by thiamine. J Biol Chem 265(19):10857–10864 Wightman R, Meacock PA (2003) The THI5 gene family of Saccharomyces cerevisiae: distribution of homologues among the hemiascomycetes and functional redundancy in the aerobic biosynthesis of thiamin from pyridoxine. Microbiology 149(Pt 6):1447–1460 Zhang RG, Skarina T, Katz JE, Beasley S, Khachatryan A, Vyas S, Arrowsmith CH, Clarke S, Edwards A, Joachimiak A et al (2001) Structure of thermo toga maritima stationary phase survival protein SurE: a novel acid phosphatase. Structure 9(11):1095–1106 Eschenfeldt WH, Lucy S, Millard CS, Joachimiak A, Mark ID (2009) A family of LIC vectors for high-throughput cloning and purification of proteins. Methods Mol Biol 498:105–115 Aslanidis C, de Jong PJ (1990) Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res 18(20):6069–6074 Haun RS, Serventi IM, Moss J (1992) Rapid, reliable ligation-independent cloning of PCR products using modified plasmid vectors. Biotechniques 13(4):515–518 Rosenbaum G, Alkire RW, Evans G, Rotella FJ, Lazarski K, Zhang RG, Ginell SL, Duke N, Naday I, Lazarz J et al (2006) The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results. J Synchrotron Radiat 13(Pt 1):30–45 Minor W, Cymborowski M, Otwinowski Z, Chruszcz M (2006) HKL-3000: the integration of data reduction and structure solution—from diffraction images to an initial model in minutes. Acta Crystallogr D Biol Crystallogr 62:859–866 Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64:112–122 Bjellqvist B, Basse B, Olsen E, Celis JE (1994) Reference points for comparisons of 2-dimensional maps of proteins from different human cell-types defined in a Ph scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 15(3–4):529–539 Terwilliger T (2004) SOLVE and RESOLVE: automated structure solution, density modification, and model building. J Synchrotron Radiat 11:49–52 Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr 67(Pt 4):355–367 Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132 Chen VB, Arendall WB III, 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 D 66:12–21 Yang HW, Guranovic V, Dutta S, Feng ZK, Berman HM, Westbrook JD (2004) Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr D Biol Crystallogr 60:1833–1839 Altschul SF, Madden TL, Schaffer 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(17):3389–3402 Soding J (2005) Protein homology detection by HMM–HMM comparison. Bioinformatics 21(7):951–960 Soding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33(Web Server issue):W244–W248 Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 1):2256–2268 Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425 Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. Academic Press, New York Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739 Kosinski J, Cymerman IA, Feder M, Kurowski MA, Sasin JM, Bujnicki JM (2003) A “FRankenstein’s monster” approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation. Proteins 53(Suppl 6):369–379 Wallner B, Elofsson A (2007) Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins 69(Suppl 8):184–193 Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM (2008) MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics 9:403 Li Z, Ye Y, Godzik A (2006) Flexible structural neighbourhood: a database of proteins structural similarities and alignments. Nucleic Acids Res 34:D277–D280 Sonnhammer EL, Eddy SR, Durbin R (1997) Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28(3):405–420 Santini S, Claverie JM, Mouz N, Rousselle T, Maza C, Monchois V, Abergel C (2011) The conserved Candida albicans CA3427 gene product defines a new family of proteins exhibiting the generic periplasmic binding protein structural fold. PLoS ONE 6(4):e18528