Garriga Damià, Navarro Aitor, Querol-Audí Jordi, Abaitua Fernando, Rodríguez José F, Verdaguer Núria
Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Cientificas, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain.
Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20540-5. doi: 10.1073/pnas.0704447104. Epub 2007 Dec 11.
Two lineages of viral RNA-dependent RNA polymerases (RDRPs) differing in the organization (canonical vs. noncanonical) of the palm subdomain have been identified. Phylogenetic analyses indicate that both lineages diverged at a very early stage of the evolution of the enzyme [Gorbalenya AE, Pringle FM, Zeddam JL, Luke BT, Cameron CE, Kalmakoff J, Hanzlik TN, Gordon KH, Ward VK (2002) J Mol Biol 324:47-62]. Here, we report the x-ray structure of a noncanonical birnaviral RDRP, named VP1, in its free form, bound to Mg(2+) ions, and bound to a peptide representing the polymerase-binding motif of the regulatory viral protein VP3. The structure of VP1 reveals that the noncanonical connectivity of the palm subdomain maintains the geometry of the catalytic residues found in canonical polymerases but results in a partial blocking of the active site cavity. The VP1-VP3 peptide complex shows a mode of polymerase activation in which VP3 binding promotes a conformational change that removes the steric blockade of the VP1 active site, facilitating the accommodation of the template and incoming nucleotides for catalysis. The striking structural similarities between birnavirus (dsRNA) and the positive-stranded RNA picornavirus and calicivirus RDRPs provide evidence supporting the existence of functional and evolutionary relationships between these two virus groups.
现已鉴定出两种病毒RNA依赖性RNA聚合酶（RDRP）谱系，其掌状亚结构域的组织方式（典型与非典型）不同。系统发育分析表明，这两种谱系在该酶进化的非常早期阶段就已分化[戈尔巴连亚AE、普林格尔FM、泽丹JL、卢克BT、卡梅伦CE、卡尔马科夫J、汉兹利克TN、戈登KH、沃德VK（2002年）《分子生物学杂志》324卷：47 - 62页]。在此，我们报告了一种非典型双RNA病毒RDRP（名为VP1）的X射线结构，其分别处于游离形式、与镁离子结合以及与代表调节性病毒蛋白VP3的聚合酶结合基序的肽结合的状态。VP1的结构表明，掌状亚结构域的非典型连接性维持了典型聚合酶中催化残基的几何形状，但导致活性位点腔部分受阻。VP1 - VP3肽复合物显示出一种聚合酶激活模式，其中VP3结合促进构象变化，消除VP1活性位点的空间位阻，便于模板和进入的核苷酸进入以进行催化。双RNA病毒（双链RNA）与正链RNA微小核糖核酸病毒和杯状病毒RDRP之间惊人的结构相似性提供了证据，支持这两个病毒组之间存在功能和进化关系。
