Wheatley Nicole M, Eden Kevin D, Ngo Joanna, Rosinski Justin S, Sawaya Michael R, Cascio Duilio, Collazo Michael, Hoveida Hamidreza, Hubbell Wayne L, Yeates Todd O
UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA.
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
J Mol Biol. 2016 Oct 9;428(20):4013-4030. doi: 10.1016/j.jmb.2016.07.015. Epub 2016 Jul 25.
Autotrophic bacteria rely on various mechanisms to increase intracellular concentrations of inorganic forms of carbon (i.e., bicarbonate and CO) in order to improve the efficiency with which they can be converted to organic forms. Transmembrane bicarbonate transporters and carboxysomes play key roles in accumulating bicarbonate and CO, but other regulatory elements of carbon concentration mechanisms in bacteria are less understood. In this study, after analyzing the genomic regions around α-type carboxysome operons, we characterize a protein that is conserved across these operons but has not been previously studied. On the basis of a series of apo- and ligand-bound crystal structures and supporting biochemical data, we show that this protein, which we refer to as the carboxysome-associated PII protein (CPII), represents a new and distinct subfamily within the broad superfamily of previously studied PII regulatory proteins, which are generally involved in regulating nitrogen metabolism in bacteria. CPII undergoes dramatic conformational changes in response to ADP binding, and the affinity for nucleotide binding is strongly enhanced by the presence of bicarbonate. CPII therefore appears to be a unique type of PII protein that senses bicarbonate availability, consistent with its apparent genomic association with the carboxysome and its constituents.
自养细菌依靠多种机制来提高细胞内无机碳形式（即碳酸氢盐和CO）的浓度，以提高它们转化为有机形式的效率。跨膜碳酸氢盐转运蛋白和羧酶体在积累碳酸氢盐和CO方面发挥关键作用，但细菌中碳浓缩机制的其他调控元件尚不太清楚。在本研究中，通过分析α型羧酶体操纵子周围的基因组区域，我们鉴定了一种在这些操纵子中保守但此前未被研究过的蛋白质。基于一系列无配体和结合配体的晶体结构以及支持性的生化数据，我们表明这种蛋白质，我们称之为羧酶体相关PII蛋白（CPII），在先前研究的PII调控蛋白的广泛超家族中代表一个新的独特亚家族，这些蛋白通常参与调节细菌中的氮代谢。CPII响应ADP结合会发生显著的构象变化，并且碳酸氢盐的存在会强烈增强其对核苷酸结合的亲和力。因此，CPII似乎是一种独特类型的PII蛋白，可感知碳酸氢盐的可用性，这与其与羧酶体及其成分明显的基因组关联一致。
