Structure of the nuclease subunit of human mitochondrial RNase P

Nucleic Acids Research

Volumn 43, Issue 11, 2015, Pages 5664-5672

  Reinhard, Linda ^a,b   Sridhara, Sagar ^a,b   Hällberg, B Martin ^a,b,c  

^a KAROLINSKA INSTITUTE   (Sweden)

^b Centre for Structural Systems Biology (CSSB HZI)   (Germany)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL RNA; MITOCHONDRIAL RNASE P PROTEIN 1; MITOCHONDRIAL RNASE P PROTEIN 2; MITOCHONDRIAL RNASE P PROTEIN 3; NUCLEASE; PLANT AND TRYPANOSOMAL RNASE P; RIBONUCLEASE P; RIBOSOME RNA; TRANSFER RNA; UNCLASSIFIED DRUG; ARABIDOPSIS PROTEIN; KIAA0391 PROTEIN, HUMAN; PRORP1 PROTEIN, ARABIDOPSIS; PROTEIN SUBUNIT;

5' UNTRANSLATED REGION; ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; BINDING SITE; CONTROLLED STUDY; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; HUMAN; HYDROGEN BOND; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; RNA PROCESSING; STRUCTURE ANALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN SUBUNIT; PROTEIN TERTIARY STRUCTURE;

ARABIDOPSIS PROTEINS; CATALYTIC DOMAIN; HUMANS; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; RIBONUCLEASE P;

EID: 84936868909     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv481     Document Type: Article

References (29)

1. Ojala, D., Montoya, J. and Attardi, G. (1981) tRNA punctuation model of RNA processing in human mitochondria. Nature, 290, 470-474.
2. Rorbach, J. and Minczuk, M. (2012) The post-transcriptional life of mammalian mitochondrial RNA. Biochem. J., 444, 357-373.
3. Rackham, O., Mercer, T.R. and Filipovska, A. (2012) The human mitochondrial transcriptome and the RNA-binding proteins that regulate its expression. Wiley Interdiscip. Rev. RNA, 3, 675-695.
4. Bogenhagen, D.F., Martin, D.W. and Koller, A. (2014) Initial steps in RNA processing and ribosome assembly occur at mitochondrial DNA nucleoids. Cell Metab., 19, 618-629.
5. Hallberg, B.M. and Larsson, N.G. (2014) Making proteins in the powerhouse. Cell Metab., 20, 226-240.
6. Holzmann, J., Frank, P., Loffer, E., Bennett, K.L., Gerner, C. and Rossmanith, W. (2008) RNase P without RNA: identifcation and functional reconstitution of the human mitochondrial tRNA processing enzyme. Cell, 135, 462-474.
7. Helm, M., Brule, H., Degoul, F., Cepanec, C., Leroux, J.P., Giege, R. and Florentz, C. (1998) The presence of modifed nucleotides is required for cloverleaf folding of a human mitochondrial tRNA. Nucleic Acids Res., 26, 1636-1643.
8. Helm, M., Giege, R. and Florentz, C. (1999) A Watson-Crick base-pair-disrupting methyl group (m1A9) is suffcient for cloverleaf folding of human mitochondrial tRNALys. Biochemistry, 38, 13338-13346.
9. Vilardo, E., Nachbagauer, C, Buzet, A., Taschner, A., Holzmann, J. and Rossmanith, W. (2012) A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase-extensive moonlighting in mitochondrial tRNA biogenesis. Nucleic Acids Res., 40, 11583-11593.
10. Suzuki, T., Nagao, A. and Suzuki, T. (2011) Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases. Annu. Rev. Genet., 45, 299-329.
11. Small, I.D. and Peeters, N. (2000) The PPR motif-a TPR-related motif prevalent in plant organellar proteins. Trends Biochem. Sci., 25, 46-47.
12. Rossmanith, W. (2012) Of P and Z: mitochondrial tRNA processing enzymes. Biochim. Biophys. Acta, 1819, 1017-1026.
13. Gobert, A., Gutmann, B., Taschner, A., Gossringer, M., Holzmann, J., Hartmann, R.K., Rossmanith, W. and Giege, P (2010) A single Arabidopsis organellar protein has RNase P activity. Nat. Struct. Mol. Biol., 17, 740-744.
14. Taschner, A., Weber, C, Buzet, A., Hartmann, R.K., Hartig, A. and Rossmanith, W. (2012) Nuclear RNase P of Trypanosoma brucei: a single protein in place of the multicomponent RNA-protein complex. Cell Rep., 2, 19-25.
15. Gutmann, B., Gobert, A. and Giege, P (2012) PRORP proteins support RNase P activity in both organelles and the nucleus in Arabidopsis. Genes Dev., 26, 1022-1027.
16. Goldfarb, K.C, Borah, S. and Cech, TR. (2012) RNase P branches out from RNP to protein: organelle-triggered diversifcation? Genes Dev., 26, 1005-1009.
17. Howard, M.J., Lim, W.H, Fierke, C.A. and Koutmos, M. (2012) Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing. Proc. Natl Acad. Sci. U.S.A., 109, 16149-16154.
18. Anantharaman, V. and Aravind, L. (2006) The NYN domains: novel predicted RNAses with a PIN domain-like fold. RNA Biol, 3, 18-27.
19. Imai, T, Nakamura, T, Maeda, T, Nakayama, K., Gao, X., Nakashima, T, Kakuta, Y. and Kimura, M. (2014) Pentatricopeptide repeat motifs in the processing enzyme PRORP1 in Arabidopsis thaliana play a crucial role in recognition of nucleotide bases at TpsiC loop in precursor tRNAs. Biochem. Biophys. Res. Commun., 450, 1541-1546.
20. Gobert, A., Pinker, F., Fuchsbauer, O., Gutmann, B., Boutin, R., Roblin, P., Sauter, C. and Giege, P. (2013) Structural insights into protein-only RNase P complexed with tRNA. Nat. Commun., 4, 1353.
21. de Sanctis, D., Beteva, A., Caserotto, H., Dobias, F., Gabadinho, J., Giraud, T., Gobbo, A., Guijarro, M., Lentini, M., Lavault, B. et al. (2012) ID29: a high-intensity highly automated ESRF beamline for macromolecular crystallography experiments exploiting anomalous scattering. J. Synchrotron. Radiat., 19, 455-461.
22. Mueller, U., Darowski, N., Fuchs, M.R., Forster, R., Hellmig, M., Paithankar, K.S., Puhringer, S., Steffen, M., Zocher, G. and Weiss, M.S. (2012) Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin. J. Synchrotron. Radiat., 19, 442-449.
23. Kabsch, W. (2010) XDS. Acta Crystallogr. D Biol. Crystallogr., 66, 125-132.
24. Karplus, P.A. and Diederichs, K. (2012) Linking crystallographic model and data quality. Science, 336, 1030-1033.
25. Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W. et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr., 66, 213-221.
26. Emsley, P., Lohkamp, B., Scott, W.G. and Cowtan, K. (2010) Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr., 66, 486-501.
27. Chen, V.B., Arendall, W.B. 3rd, Headd, J.J., Keedy, D.A., Immormino, R.M., Kapral, G.J., Murray, L.W., Richardson, J.S. and Richardson, D.C. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr., 66, 12-21.
28. Batey, R.T. and Kieft, J.S. (2007) Improved native affnity purifcation of RNA. RNA, 13, 1384-1389.
29. Howard, M.J., Klemm, B.P. and Fierke, C.A. (2015) Mechanistic studies reveal similar catalytic strategies for phosphodiester bond hydrolysis by protein-only and RNA-dependent Ribonuclease P. J. Biol. Chem., doi:10.1074/jbc.M115.644831.