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Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum
Department of Chemistry and Biochemistry and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH 45056, USA
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Campbell Family Cancer Research Institute, Ontario Cancer Institute and the Northeast Structural Genomics Consortium, University Health Network, Toronto, ON, M5G 2C4, Canada
* Author to whom correspondence should be addressed.
Received: 20 April 2012; in revised form: 25 May 2012 / Accepted: 4 June 2012 / Published: 14 June 2012
Abstract: CV_2116 is a small hypothetical protein of 82 amino acids from the Gram-negative coccobacillus Chromobacterium violaceum. A PSI-BLAST search using the CV_2116 sequence as a query identified only one hit (E = 2e−07) corresponding to a hypothetical protein OR16_04617 from Cupriavidus basilensis OR16, which failed to provide insight into the function of CV_2116. The CV_2116 gene was cloned into the p15TvLic expression plasmid, transformed into E. coli, and 13C- and 15N-labeled NMR samples of CV_2116 were overexpressed in E. coli and purified for structure determination using NMR spectroscopy. The resulting high-quality solution NMR structure of CV_2116 revealed a novel α + β fold containing two anti-parallel β -sheets in the N-terminal two-thirds of the protein and one α-helix in the C-terminal third of the protein. CV_2116 does not belong to any known protein sequence family and a Dali search indicated that no similar structures exist in the protein data bank. Although no function of CV_2116 could be derived from either sequence or structural similarity searches, the neighboring genes of CV_2116 encode various proteins annotated as similar to bacteriophage tail assembly proteins. Interestingly, C. violaceum exhibits an extensive network of bacteriophage tail-like structures that likely result from lateral gene transfer by incorporation of viral DNA into its genome (prophages) due to bacteriophage infection. Indeed, C. violaceum has been shown to contain four prophage elements and CV_2116 resides in the fourth of these elements. Analysis of the putative operon in which CV_2116 resides indicates that CV_2116 might be a component of the bacteriophage tail-like assembly that occurs in C. violaceum.
Keywords: CV_2116; Chromobacterium violaceum; NMR; solution structure; structural genomics; bacteriophage tail assembly; prophage; lateral gene transfer
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Yang, Y.; Ramelot, T.A.; Cort, J.R.; Garcia, M.; Yee, A.; Arrowsmith, C.H.; Kennedy, M.A. Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum. Int. J. Mol. Sci. 2012, 13, 7354-7364.
Yang Y, Ramelot TA, Cort JR, Garcia M, Yee A, Arrowsmith CH, Kennedy MA. Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum. International Journal of Molecular Sciences. 2012; 13(6):7354-7364.
Yang, Yunhuang; Ramelot, Theresa A.; Cort, John R.; Garcia, Maite; Yee, Adelinda; Arrowsmith, Cheryl H.; Kennedy, Michael A. 2012. "Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum." Int. J. Mol. Sci. 13, no. 6: 7354-7364.