Rohnke Brandon A, Kerfeld Cheryl A, Montgomery Beronda L
MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States.
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States.
Front Microbiol. 2020 Feb 28;11:187. doi: 10.3389/fmicb.2020.00187. eCollection 2020.
Two proteins found in cyanobacteria contain a C-terminal domain with homology to the small subunit of rubisco (RbcS). These small subunit-like domains (SSLDs) are important features of CcmM, a protein involved in the biogenesis of carboxysomes found in all β-cyanobacteria, and a rubisco activase homolog [activase-like protein of cyanobacteria (ALC)] found in over a third of sequenced cyanobacterial genomes. Interaction with rubisco is crucial to the function of CcmM and is believed to be important to ALC as well. In both cases, the SSLD aggregates rubisco, and this nucleation event may be important in regulating rubisco assembly and activity. Recently, two independent studies supported the conclusion that the SSLD of CcmM binds equatorially to LS holoenzymes of rubisco rather than by displacing an RbcS, as its structural homology would suggest. We use sequence analysis and homology modeling to examine whether the SSLD from the ALC could bind the large subunit of rubisco either via an equatorial interaction or in an RbcS site, if available. We suggest that the SSLD from the ALC of could bind either in a vacant RbcS site or equatorially. Our homology modeling takes into account N-terminal residues not represented in available cryo-electron microscopy structures that potentially contribute to the interface between the large subunit of rubisco (RbcL) and RbcS. Here, we suggest the perspective that binding site variability as a means of regulation is plausible and that the dynamic interaction between the RbcL, RbcS, and SSLDs may be important for carboxysome assembly and function.
在蓝细菌中发现的两种蛋白质含有一个与核酮糖-1,5-二磷酸羧化酶小亚基（RbcS）具有同源性的C末端结构域。这些小亚基样结构域（SSLDs）是CcmM的重要特征，CcmM是一种参与所有β-蓝细菌中羧酶体生物合成的蛋白质，以及在超过三分之一的已测序蓝细菌基因组中发现的一种核酮糖-1,5-二磷酸羧化酶激活酶同源物[蓝细菌激活酶样蛋白（ALC）]。与核酮糖-1,5-二磷酸羧化酶的相互作用对CcmM的功能至关重要，并且据信对ALC也很重要。在这两种情况下，SSLD都会使核酮糖-1,5-二磷酸羧化酶聚集，并且这种成核事件可能对调节核酮糖-1,5-二磷酸羧化酶的组装和活性很重要。最近，两项独立研究支持了这样的结论，即CcmM的SSLD与核酮糖-1,5-二磷酸羧化酶的LS全酶赤道结合，而不是像其结构同源性所暗示的那样取代一个RbcS。我们使用序列分析和同源建模来研究来自ALC的SSLD是否可以通过赤道相互作用或在RbcS位点（如果可用）结合核酮糖-1,5-二磷酸羧化酶的大亚基。我们认为来自ALC的SSLD可以在空的RbcS位点或赤道结合。我们的同源建模考虑了现有冷冻电子显微镜结构中未显示的N末端残基，这些残基可能有助于核酮糖-1,5-二磷酸羧化酶大亚基（RbcL）和RbcS之间的界面。在这里，我们提出这样一种观点，即作为一种调节手段的结合位点变异性是合理的，并且RbcL、RbcS和SSLDs之间的动态相互作用可能对羧酶体的组装和功能很重要。
