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Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus.

Ishii R, Nureki O, Yokoyama S
J Biol Chem 278 32397-404 (2003)
Related entries: 1udo, 1udq, 1uds

Cited: 28 times
EuropePMC logo PMID: 12746447

Abstract

RNase PH is one of the exoribonucleases that catalyze the 3' end processing of tRNA in bacteria. RNase PH removes nucleotides following the CCA sequence of tRNA precursors by phosphorolysis and generates mature tRNAs with amino acid acceptor activity. In this study, we determined the crystal structure of Aquifex aeolicus RNase PH bound with a phosphate, a co-substrate, in the active site at 2.3-A resolution. RNase PH has the typical alpha/beta fold, which forms a hexameric ring structure as a trimer of dimers. This ring structure resembles that of the polynucleotide phosphorylase core domain homotrimer, another phosphorolytic exoribonuclease. Four amino acid residues, Arg-86, Gly-124, Thr-125, and Arg-126, of RNase PH are involved in the phosphate-binding site. Mutational analyses of these residues showed their importance in the phosphorolysis reaction. A docking model with the tRNA acceptor stem suggests how RNase PH accommodates substrate RNAs.

Reviews - 1udn mentioned but not cited (2)

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  2. Structural components and architectures of RNA exosomes. Januszyk K, Lima CD. Adv Exp Med Biol 702 9-28 (2010)

Articles - 1udn mentioned but not cited (1)

  1. Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding. Harlow LS, Kadziola A, Jensen KF, Larsen S. Protein Sci 13 668-677 (2004)


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  1. The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Lorentzen E, Walter P, Fribourg S, Evguenieva-Hackenberg E, Klug G, Conti E. Nat Struct Mol Biol 12 575-581 (2005)
  2. Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly. Nurmohamed S, Vaidialingam B, Callaghan AJ, Luisi BF. J Mol Biol 389 17-33 (2009)
  3. The Phosphorolytic Exoribonucleases Polynucleotide Phosphorylase and RNase PH Stabilize sRNAs and Facilitate Regulation of Their mRNA Targets. Cameron TA, De Lay NR. J Bacteriol 198 3309-3317 (2016)
  4. Structure and Activities of the Eukaryotic RNA Exosome. Wasmuth EV, Lima CD. Enzymes 31 53-75 (2012)
  5. Structural and biochemical characterization of CRN-5 and Rrp46: an exosome component participating in apoptotic DNA degradation. Yang CC, Wang YT, Hsiao YY, Doudeva LG, Kuo PH, Chow SY, Yuan HS. RNA 16 1748-1759 (2010)
  6. The oligomeric architecture of the archaeal exosome is important for processive and efficient RNA degradation. Audin MJ, Wurm JP, Cvetkovic MA, Sprangers R. Nucleic Acids Res 44 2962-2973 (2016)
  7. Polynucleotide phosphorylase interacts with ribonuclease E through a betabetaalphabetabetaalpha domain. Durán-Figueroa NV, Piña-Escobedo A, Schroeder I, Simons RW, García-Mena J. Biochimie 88 725-735 (2006)
  8. Structure of the Methanothermobacter thermautotrophicus exosome RNase PH ring. Ng CL, Waterman DG, Antson AA, Ortiz-Lombardía M. Acta Crystallogr D Biol Crystallogr 66 522-528 (2010)
  9. An amino acid code for irregular and mixed protein packing. Joo H, Chavan AG, Fraga KJ, Tsai J. Proteins 83 2147-2161 (2015)
  10. Enhanced Symbiotic Characteristics in Bacterial Genomes with the Disruption of rRNA Operon. Ahn H, Seol D, Cho S, Kim H, Kwak W. Biology (Basel) 9 E440 (2020)
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  12. Discovery and initial characterization of YloC, a novel endoribonuclease in Bacillus subtilis. Ingle S, Chhabra S, Chen J, Lazarus MB, Luo X, Bechhofer DH. RNA 28 227-238 (2022)
  13. Fine mapping of pss1, a pollen semi-sterile gene in rice (Oryza sativa L.). Li W, Jiang L, Zhou S, Wang C, Liu L, Chen L, Ikehashi H, Wan J. Theor Appl Genet 114 939-946 (2007)
  14. Bacterial RNA-free RNase P: Structural and functional characterization of multiple oligomeric forms of a minimal protein-only ribonuclease P. Wilhelm CA, Mallik L, Kelly AL, Brotzman S, Mendoza J, Anders AG, Leskaj S, Castillo C, Ruotolo BT, Cianfrocco MA, Koutmos M. J Biol Chem 299 105327 (2023)
  15. The structure of Rph, an exoribonuclease from Bacillus anthracis, at 1.7 A resolution. Rawlings AE, Blagova EV, Levdikov VM, Fogg MJ, Wilson KS, Wilkinson AJ. Acta Crystallogr Sect F Struct Biol Cryst Commun 65 2-7 (2009)


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