Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16149-54. doi: 10.1073/pnas.1209062109. Epub 2012 Sep 18.
Ribonuclease P (RNase P) catalyzes the maturation of the 5' end of tRNA precursors. Typically these enzymes are ribonucleoproteins with a conserved RNA component responsible for catalysis. However, protein-only RNase P (PRORP) enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana. PRORP enzymes are nuclear encoded and conserved among many eukaryotes, having evolved recently as yeast mitochondrial genomes encode an RNase P RNA. Here we report the crystal structure of PRORP1 from A. thaliana at 1.75 Å resolution, revealing a prototypical metallonuclease domain tethered to a pentatricopeptide repeat (PPR) domain by a structural zinc-binding domain. The metallonuclease domain is a unique high-resolution structure of a Nedd4-BP1, YacP Nucleases (NYN) domain that is a member of the PIN domain-like fold superfamily, including the FLAP nuclease family. The structural similarity between PRORP1 and the FLAP nuclease family suggests that they evolved from a common ancestor. Biochemical data reveal that conserved aspartate residues in PRORP1 are important for catalytic activity and metal binding and that the PPR domain also enhances activity, likely through an interaction with pre-tRNA. These results provide a foundation for understanding tRNA maturation in organelles. Furthermore, these studies allow for a molecular-level comparison of the catalytic strategies used by the only known naturally evolved protein and RNA-based catalysts that perform the same biological function, pre-tRNA maturation, thereby providing insight into the differences between the prebiotic RNA world and the present protein-dominated world.
核糖核酸酶 P（RNase P）催化 tRNA 前体 5'端的成熟。通常情况下，这些酶是核糖核蛋白，其中保守的 RNA 成分负责催化。然而，仅含蛋白质的 RNase P（PRORP）酶在人类线粒体和拟南芥所有使用 tRNA 的隔室中加工前体 tRNA。PRORP 酶是核编码的，在许多真核生物中保守，最近在酵母线粒体基因组中编码 RNase P RNA 时才进化而来。在这里，我们报告了来自拟南芥的 PRORP1 的晶体结构，分辨率为 1.75 Å，揭示了一个典型的金属核酸酶结构域通过结构锌结合结构域与五肽重复（PPR）结构域连接。金属核酸酶结构域是 Nedd4-BP1、YacP Nucleases（NYN）结构域的独特高分辨率结构，该结构域是 PIN 结构域样折叠超家族的成员，包括 FLAP 核酸酶家族。PRORP1 与 FLAP 核酸酶家族之间的结构相似性表明它们来自共同的祖先。生化数据表明，PRORP1 中的保守天冬氨酸残基对催化活性和金属结合很重要，并且 PPR 结构域也增强了活性，可能是通过与前 tRNA 相互作用。这些结果为理解细胞器中的 tRNA 成熟提供了基础。此外，这些研究允许对仅有的已知自然进化的蛋白质和 RNA 基催化剂在执行相同生物学功能（即前 tRNA 成熟）时使用的催化策略进行分子水平比较，从而深入了解前生物 RNA 世界和目前以蛋白质为主导的世界之间的差异。
