Crystal structure of protein Ph1481p in complex with protein Ph1877p of archaeal RNase P from Pyrococcus horikoshii OT3: Implication of dimer formation of the holoenzyme

Journal of Molecular Biology

Volumn 357, Issue 2, 2006, Pages 583-591

  Kawano, Shin ^a   Nakashima, Takashi ^a   Kakuta, Yoshimitsu ^a   Tanaka, Isao ^b   Kimura, Makoto ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Crystal structure; P. horikoshii; Protein protein interaction; Ribonuclease P; X ray analysis

Indexed keywords

HOLOENZYME; PROTEIN; PROTEIN PH1481P; PROTEIN PH1877P; RIBONUCLEASE P; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; DIMERIZATION; GEL FILTRATION CHROMATOGRAPHY; HYDROGEN BOND; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; PYROCOCCUS HORIKOSHII;

ARCHAEA; PYROCOCCUS HORIKOSHII;

EID: 33344479270     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.12.086     Document Type: Article

References (34)

1. D.N. Frank, and N.R. Pace Ribonuclase P: unity and diversity in tRNAprocessing enzyme Annu. Rev. Biochem. 67 1998 153 180
2. S. Altman, and L. Kirsebom Ribonuclase P R.F. Gesteland T. Cech J.F. Atkins The RNA world 1999 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY 351 380
3. J. Hsieh, A.J. Andrews, and C.A. Fierke Roles of protein subunits in RNA-protein complexes: lessons from ribonuclease P Biopolymers 73 2004 79 89
4. C. Guerrier-Takada, K. Gardiner, T. Marsh, N. Pace, and S. Altman The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme Cell 35 1983 849 857
5. M. Bartkiewicz, H. Gold, and S. Altman Identification and characterization of an RNA molecule that copurifies with RNase P activity from HeLa cells Genes Dev. 3 1989 488 499
6. Y. Yuan, and S. Altman Substrate recognition by human RNase P: identification of small, model substrates for the enzyme EMBO J. 14 1995 159 168
7. S. Xiao, F. Houser-Scott, and D.R. Engelke Eukaryotic ribonuclease P: Increased complexity to cope with the nuclear pre-tRNA pathway J. Cell. Physiol. 187 2001 11 20
8. H. Mann, Y. Ben-Asouli, A. Schein, S. Moussa, and N. Jarrous Eukaryotic RNase P: role of RNA and protein subunits of a primordial catalytic ribonucleo protein in RNA-based catalysis Mol. Cell 12 2003 925 935
9. Y. Kouzuma, M. Mizoguchi, H. Takagi, H. Fukuhara, M. Tsukamoto, T. Numata, and M. Kimura Reconstitution of archaeal ribonuclease P from RNA and four protein components Biochem. Biophys. Res. Commun. 306 2003 666 673
10. Y. Kakuta, I. Ishimatsu, T. Numata, I. Tanaka, and M. Kimura Crystal structure of a ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3: an archaeal homolog of human nuclear ribonuclease P protein Rpp21 Biochemistry 44 2005 12086 12093
11. T. Numata, I. Ishimatsu, Y. Kakuta, I. Tanaka, and M. Kimura Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29 RNA 10 2004 1423 1432
12. H. Takagi, M. Watanabe, Y. Kakuta, R. Kamachi, T. Numata, I. Tanaka, and M. Kimura Crystal structure of the ribonuclease P protein Ph1877p from hyperthermophilic archaeon Pyrococcus horikoshii OT3 Biochem. Biophys. Res. Commun. 319 2004 787 794
13. M. Kifusa, H. Fukuhara, T. Hayashi, and M. Kimura Protein-protein interactions in the subunits of ribonuclease P in hyperthermophilic archaeon Pyrococcus horikoshii OT3 Biosci. Biotechnol. Biochem. 69 2005 1209 1212
14. H. van Eenennaam, D. Lugtenberg, J.H.P. Vogelzangs, W.J. van Venrooij, and G.J.M. Pruijn hPop5, a protein subunit of the human RNase MRP and RNase P endoribonucleases J. Biol. Chem. 276 2001 31635 31641
15. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallog. 26 1993 283 291
16. T. Stams, S. Niranjanakumari, C.A. Fierke, and D.W. Christianson Ribonuclease P protein structure: evolutionary origins in the translational apparatus Science 280 1998 752 755
17. C. Spitzfaden, N. Nicholson, J.J. Jones, S. Guth, R. Lehr, and C.D. Prescott The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA J. Mol. Biol. 295 2000 105 115
18. A.V. Kazantsev, A.A. Krivenko, D.J. Harrington, R.J. Carter, S.R. Holbrook, P.D. Adams, and N.R. Pace High-resolution structure of RNase P protein from Thermotoga maritima Proc. Natl Acad. Sci. USA 100 2003 7497 7502
19. L. Holm, and C. Sander Protein structure comparison by alignment of distance matrices J. Mol. Biol. 233 1993 123 138
20. C.G. Burd, and G. Dreyfuss Conserved structures and diversity of functions of RNA-binding proteins Science 265 1994 615 621
21. B.A. Sosnowski, J.M. Belote, and M. Mckeown Sex-specific alternative splicing of RNA from the transformer genes results from sequence-dependent splice site blockage Cell 58 1989 449 459
22. K. Inoue, K. Hoshijima, H. Sakamoto, and Y. Shimura Binding of the Drosophila sex-lethal gene product to the alternative splice set of transformer primary transcript Nature 344 1990 461 463
23. N. Hanada, O. Nureki, K. Kurimoto, I. Kim, H. Sakamoto, and Y. Shimura Structure basis for recognition of the tra mRNA precursor by the sex-lethal protein Nature 398 1999 579 584
24. S.A. Adam, T. Nakagawa, M.S. Swanson, T.K. Woodruff, and G. Dreyfuss mRNA polyadenylate-binding protein: gene isolation and sequencing and identification of a ribonucleoprotein consensus sequence Mol. Cell. Biol. 6 1986 2932 2943
25. B.S. Baker Sex in flies: the splice of life Nature 340 1987 521 524
26. J. Hodgkin Drosophila sex determination: a cascade of regulated splicing Cell 56 1987 905 906
27. M.S. Swanson, T.Y. Nakagawa, K. LeVan, and G. Dreyfuss Primary structure of human nuclear ribonucleoprotein particle C proteins: conservation of sequence and domain structures in heterogeneous nuclear RNA, mRNA, and pre-rRNA-binding proteins Mol. Cell. Biol. 7 1987 1731 1739
28. X.-W. Fang, X.-J. Yang, K. Littrell, S. Niranjanakumari, P. Thiyagarajan, and C.A. Fierke The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits RNA 7 2001 233 241
29. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
30. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, and R.W. Grosse-Kunstleve Crystallography NMR system: a new software suite for macromolecular structure determination Acta Crystallog. sect. D 54 1998 905 921
31. A. Perrakis, R. Morris, and V.S. Lamzin Automated protein model building combined with iterative structure refinement Nature Struct. Biol. 6 1999 458 463
32. T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallog. sect. A 47 1991 110 119
33. P.J. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 946 950
34. A. Nicholls, K. Sharp, and B. Honing Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons Proteins: Struct. Funct. Genet. 11 1991 281 296