Yang Yunhuang, Ramelot Theresa A, Cort John R, Garcia Maite, Yee Adelinda, Arrowsmith Cheryl H, Kennedy Michael A
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.
Int J Mol Sci. 2012;13(6):7354-7364. doi: 10.3390/ijms13067354. Epub 2012 Jun 14.
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 (13)C- and (15)N-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.
CV_2116是一种来自革兰氏阴性球杆菌紫色色杆菌的由82个氨基酸组成的假定小蛋白。以CV_2116序列作为查询序列进行PSI-BLAST搜索，仅发现一个匹配项（E = 2e(-07)），对应于来自罗尔斯通氏菌OR16的假定蛋白OR16_04617，但这并未为CV_2116的功能提供线索。将CV_2116基因克隆到p15TvLic表达质粒中，转化到大肠杆菌中，用(13)C和(15)N标记的CV_2116核磁共振样品在大肠杆菌中过表达，并通过核磁共振光谱法纯化以确定其结构。所得的高质量CV_2116溶液核磁共振结构揭示了一种新颖的α + β折叠结构，在蛋白质N端三分之二区域包含两个反平行β折叠片层，在蛋白质C端三分之一区域包含一个α螺旋。CV_2116不属于任何已知的蛋白质序列家族，Dali搜索表明蛋白质数据库中不存在相似结构。尽管通过序列或结构相似性搜索均无法得出CV_2116的功能，但CV_2116的相邻基因编码各种注释为类似于噬菌体尾部组装蛋白的蛋白质。有趣的是，紫色色杆菌表现出广泛的噬菌体尾部样结构网络，这可能是由于噬菌体感染导致病毒DNA整合到其基因组（原噬菌体）中而通过横向基因转移产生的。实际上，已证明紫色色杆菌含有四个原噬菌体元件，而CV_2116位于这些元件中的第四个元件中。对CV_2116所在的假定操纵子的分析表明，CV_2116可能是紫色色杆菌中出现的噬菌体尾部样组装体的一个组成部分。
