Department of Microbiology, Monash University, Clayton, Victoria, Australia.
PLoS One. 2011;6(8):e23245. doi: 10.1371/journal.pone.0023245. Epub 2011 Aug 17.
The yeaZ gene product forms part of the conserved network YjeE/YeaZ/YgjD essential for the survival of many gram-negative eubacteria. Among other as yet unidentified roles, YeaZ functions as a resuscitation promoting factor required for survival and resuscitation of cells in a viable but non-culturable (VBNC) state.
METHODOLOGY/PRINCIPAL FINDINGS: In order to investigate in detail the structure/function relationship of this family of proteins we have performed X-ray crystallographic studies of Vibrio parahaemolyticus YeaZ. The YeaZ structure showed that it has a classic actin-like nucleotide-binding fold. Comparisons of this crystal structure to that of available homologues from E. coli, T. maritima and S. typhimurium revealed two distinctly different modes of dimer formation. In one form, prevalent in the absence of nucleotide, the putative nucleotide-binding site is incomplete, lacking a binding pocket for a nucleotide base. In the second form, residues from the second subunit complete the nucleotide-binding site. This suggests that the two dimer architectures observed in the crystal structures correspond to a free and a nucleotide-bound form of YeaZ. A multiple sequence alignment of YeaZ proteins from different bacteria allowed us to identify a large conserved hydrophobic patch on the protein surface that becomes exposed upon nucleotide-driven dimer re-arrangement. We hypothesize that the transition between two dimer architectures represents the transition between the 'on' and 'off' states of YeaZ. The effect of this transition is to alternately expose and bury a docking site for the partner protein YgjD.
CONCLUSIONS/SIGNIFICANCE: This paper provides the first structural insight into the putative mechanism of nucleotide regulation of YeaZ through dimer reorganization. Our analysis suggests that nucleotide binding to YeaZ may act as a regulator or switch that changes YeaZ shape, allowing it to switch partners between YjeE and YgjD.
yeaZ 基因产物是保守网络 YjeE/YeaZ/YgjD 的一部分，对许多革兰氏阴性细菌的生存至关重要。在其他尚未确定的作用中，YeaZ 作为复苏促进因子发挥作用，对于处于存活但非可培养（VBNC）状态的细胞的生存和复苏是必需的。
方法/主要发现：为了详细研究这个蛋白质家族的结构/功能关系，我们对副溶血性弧菌 YeaZ 进行了 X 射线晶体学研究。YeaZ 结构表明它具有经典的肌动蛋白样核苷酸结合折叠。将这个晶体结构与来自大肠杆菌、T. maritima 和 S. typhimurium 的现有同源物的结构进行比较，揭示了两种截然不同的二聚体形成方式。在一种形式中，在没有核苷酸的情况下，假定的核苷酸结合位点不完整，缺乏核苷酸碱基的结合口袋。在第二种形式中，来自第二个亚基的残基完成了核苷酸结合位点。这表明晶体结构中观察到的两种二聚体结构对应于 YeaZ 的自由和核苷酸结合形式。来自不同细菌的 YeaZ 蛋白质的多重序列比对使我们能够识别蛋白质表面上的一个大的保守疏水斑块，该斑块在核苷酸驱动的二聚体重新排列时暴露出来。我们假设，两种二聚体结构之间的转变代表了 YeaZ 的“开”和“关”状态之间的转变。这种转变的效果是交替暴露和埋藏伴侣蛋白 YgjD 的对接位点。
结论/意义：本文首次提供了关于核苷酸调节 YeaZ 通过二聚体重组的潜在机制的结构见解。我们的分析表明，核苷酸与 YeaZ 的结合可能作为一种调节剂或开关，改变 YeaZ 的形状，使其能够在 YjeE 和 YgjD 之间切换伴侣。
