Crystal structure of the RNA 2′-phosphotransferase from Aeropyrum pernix K1

Journal of Molecular Biology

Volumn 348, Issue 2, 2005, Pages 295-305

  Kato Murayama, Miyuki ^a   Bessho, Yoshitaka ^a   Shirouzu, Mikako ^a,b   Yokoyama, Shigeyuki ^a,b,c  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

^b RIKEN HARIMA INSTITUTE   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

2 Phosphotransferase; ADP ribosylating enzyme; NAD binding protein; tRNA splicing; Winged helix

Indexed keywords

ADENOSINE DIPHOSPHATE RIBOSE; BACTERIAL ENZYME; BACTERIAL TOXIN; DIPHTHERIA TOXIN; DNA BINDING PROTEIN; NICOTINAMIDE ADENINE DINUCLEOTIDE; PHOSPHOTRANSFERASE; RNA 2' PHOSPHOTRANSFERASE; SUGAR PHOSPHATE; TRANSFER RNA; UNCLASSIFIED DRUG;

AEROPYRUM; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CRYSTAL STRUCTURE; ENZYME ANALYSIS; ENZYME BINDING; ENZYME STRUCTURE; ENZYME SUBSTRATE; MOLECULAR RECOGNITION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN TARGETING;

EID: 16244403340     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.02.049     Document Type: Article

References (65)

1. K. Kleman-Leyer, D.W. Armbruster, and C.J. Daniels Properties of H. volcanii tRNA intron endonuclease reveal a relationship between the archaeal and eucaryal tRNA intron processing systems Cell 89 1997 839 847
2. C.R. Trotta, F. Miao, E.A. Arn, S.W. Stevens, C.K. Ho, R. Rauhut, and J.N. Abelson The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases Cell 89 1997 849 858
3. J. Lykke-Andersen, and R.A. Garrett RNA-protein interactions of an archaeal homotetrameric splicing endoribonuclease with an exceptional evolutionary history EMBO J. 16 1997 6290 6300
4. H. Li, C.R. Trotta, and J. Abelson Crystal structure and evolution of a transfer RNA splicing enzyme Science 280 1998 279 284
5. H. Li, and J. Abelson Crystal structure of a dimeric archaeal splicing endonuclease J. Mol. Biol. 302 2000 639 648
6. C.L. Greer, C.L. Peebles, P. Gegenheimer, and J. Abelson Mechanism of action of a yeast RNA ligase in tRNA splicing Cell 32 1983 537 546
7. E.M. Phizicky, S.A. Consaul, K.W. Nehrke, and J. Abelson Yeast tRNA ligase mutants are nonviable and accumulate tRNA splicing intermediates J. Biol. Chem. 267 1992 4577 4582
8. S.K. Westaway, H.G. Belford, B.L. Apostol, J. Abelson, and C.L. Greer Novel activity of a yeast ligase deletion polypeptide. Evidence for GTP-dependent tRNA splicing J. Biol. Chem. 268 1993 2435 2443
9. H.G. Belford, S.K. Westaway, J. Abelson, and C.L. Greer Multiple nucleotide cofactor use by yeast ligase in tRNA splicing. Evidence for independent ATP- and GTP-binding sites J. Biol. Chem. 268 1993 2444 2450
10. S.M. McCraith, and E.M. Phizicky A highly specific phosphatase from Saccharomyces cerevisiae implicated in tRNA splicing Mol. Cell. Biol. 10 1990 1049 1055
11. S.M. McCraith, and E.M. Phizicky An enzyme from Saccharomyces cerevisiae uses NAD+ to transfer the splice junction 2′-phosphate from ligated tRNA to an acceptor molecule J. Biol. Chem. 266 1991 11986 11992
12. G.M. Culver, S.M. McCraith, M. Zillmann, R. Kierzek, N. Michaud, and R.D. LaReau An NAD derivative produced during transfer RNA splicing: ADP-ribose 1″-2″ cyclic phosphate Science 261 1993 206 208
13. S.L. Spinelli, S.A. Consaul, and E.M. Phizicky A conditional lethal yeast phosphotransferase (tpt1) mutant accumulates tRNAs with a 2′-phosphate and an undermodified base at the splice junction RNA 3 1997 1388 1400
14. K. Nishikura, and E.M. De Robertis RNA processing in microinjected Xenopus oocytes. Sequential addition of base modifications in the spliced transfer RNA J. Mol. Biol. 145 1981 405 420
15. W. Filipowicz, M. Konarska, H.J. Gross, and A.J. Shatkin RNA 3′-terminal phosphate cyclase activity and RNA ligation in HeLa cell extract Nucl. Acids Res. 11 1983 1405 1418
16. F.A. Laski, A.Z. Fire, U.L. RajBhandary, and P.A. Sharp Characterization of tRNA precursor splicing in mammalian extracts J. Biol. Chem. 258 1983 11974 11980
17. R.C. Schwartz, C.L. Greer, P. Gegenheimer, and J. Abelson Enzymatic mechanism of an RNA ligase from wheat germ J. Biol. Chem. 258 1983 8374 8383
18. L. Pick, H. Furneaux, and J. Hurwitz Purification of wheat germ RNA ligase. II. Mechanism of action of wheat germ RNA ligase J. Biol. Chem. 261 1986 6694 6704
19. L. Pick, and J. Hurwitz Purification of wheat germ RNA ligase. I. Characterization of a ligase-associated 5′-hydroxyl polynucleotide kinase activity J. Biol. Chem. 261 1986 6684 6693
20. Y. Kikuchi, K. Tyc, W. Filipowicz, H.L. Sanger, and H.J. Gross Circularization of linear viroid RNA via 2′-phosphomonoester, 3′, 5′-phosphodiester bonds by a novel type of RNA ligase from wheat germ and Chlamydomonas Nucl. Acids Res. 10 1982 7521 7529
21. M. Zillmann, M.A. Gorovsky, and E.M. Phizicky Conserved mechanism of tRNA splicing in eukaryotes Mol. Cell. Biol. 11 1991 5410 5416
22. M. Zillman, M.A. Gorovsky, and E.M. Phizicky HeLa cells contain a 2′-phosphate-specific phosphotransferase similar to a yeast enzyme implicated in tRNA splicing J. Biol. Chem. 267 1992 10289 10294
23. C. Marck, and H. Grosjean Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications RNA 9 2003 1516 1531
24. J.M. Bujnicki, and L. Rychlewski Prediction of a common fold for all four subunits of the yeast tRNA splicing endonuclease: implications for the evolution of the EndA/Sen family FEBS Letters 486 2000 328 329
25. I. Gomes, and R. Gupta RNA splicing ligase activity in the archaeon Haloferax volcanii Biochem. Biophys. Res. Commun. 237 1997 588 594
26. L. Zofallova, Y. Guo, and R. Gupta Junction phosphate is derived from the precursor in the tRNA spliced by the archaeon Haloferax volcanii cell extract RNA 6 2000 1019 1030
27. E.A. Arn, and J.N. Abelson The 2′-5′ RNA ligase of Escherichia coli. Purification, cloning, and genomic disruption J. Biol. Chem. 271 1996 31145 31153
28. M. Kato, M. Shirouzu, T. Terada, H. Yamaguchi, K. Murayama, and H. Sakai Crystal structure of the 2′-5′ RNA ligase from Thermus thermophilus HB8 J. Mol. Biol. 329 2003 903 911
29. S.L. Spinelli, H.S. Malik, S.A. Consaul, and E.M. Phizicky A functional homolog of a yeast tRNA splicing enzyme is conserved in higher eukaryotes and in Escherichia coli Proc. Natl Acad. Sci. USA 95 1998 14136 14141
30. T.N. Gonzalez, C. Sidrauski, S. Dorfler, and P. Walter Mechanism of non-spliceosomal mRNA splicing in the unfolded protein response pathway EMBO J. 18 1999 3119 3132
31. J. Qi, M.N. Isupov, J.A. Littlechild, and L.E. Anderson Chloroplast glyceraldehyde-3-phosphate dehydrogenase contains a single disulfide bond located in the C-terminal extension to the B subunit J. Biol. Chem. 276 2001 35247 35252
32. K. Ogasahara, N.N. Khechinashvili, M. Nakamura, T. Yoshimoto, and K. Yutani Thermal stability of pyrrolidone carboxyl peptidases from the hyperthermophilic Archaeon, Pyrococcus furiosus Eur. J. Biochem. 268 2001 3233 3242
33. L. Holm, and C. Sander Protein structure comparison by alignment of distance matrices J. Mol. Biol. 233 1993 123 138
34. K.S. Gajiwala, and S.K. Burley Winged helix proteins Curr. Opin. Struct. Biol. 10 2000 110 116
35. Y. Mo, W. Ho, K. Johnston, and R. Marmorstein Crystal structure of a ternary SAP-1/SRF/c-fos SRE DNA complex J. Mol. Biol. 314 2001 495 506
36. M. Selmer, and X.D. Su Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB EMBO J. 21 2002 4145 4153
37. C. Alfano, D. Sanfelice, J. Babon, G. Kelly, A. Jacks, S. Curry, and M.R. Conte Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein Nature Struct. Mol. Biol. 11 2004 323 329
38. G. Dong, G. Chakshusmathi, S.L. Wolin, and K.M. Reinisch Structure of the La motif: a winged helix domain mediates RNA binding via a conserved aromatic patch EMBO J. 23 2004 1000 1007
39. Z. Wei, P. Zhang, Z. Zhou, Z. Cheng, M. Wan, and W. Gong Crystal structure of human eIF3k, the first structure of eIF3 subunits J. Biol. Chem. 279 2004 34983 34990
40. C.R. Bellamacina The nicotinamide dinucleotide binding motif: a comparison of nucleotide binding proteins FASEB J. 10 1996 1257 1269
41. A. Bateman, L. Coin, R. Durbin, R.D. Finn, V. Hollich, and S. Griffiths-Jones The Pfam protein families database Nucl. Acids Res. 32 2004 D138 D141
42. M. Domenighini, and R. Rappuoli Three conserved consensus sequences identify the NAD-binding site of ADP-ribosylating enzymes, expressed by eukaryotes, bacteria and T-even bacteriophages Mol. Microbiol. 21 1996 667 674
43. C.E. Bell, and D. Eisenberg Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide Biochemistry 35 1996 1137 1149
44. R.G. Zhang, D.L. Scott, M.L. Westbrook, S. Nance, B.D. Spangler, G.G. Shipley, and E.M. Westbrook The three-dimensional crystal structure of cholera toxin J. Mol. Biol. 251 1995 563 573
45. P.E. Stein, A. Boodhoo, G.D. Armstrong, S.A. Cockle, M.H. Klein, and R.J. Read The crystal structure of pertussis toxin Structure 2 1994 45 57
46. T.K. Sixma, K.H. Kalk, B.A. van Zanten, Z. Dauter, J. Kingma, B. Witholt, and W.G. Hol Refined structure of Escherichia coli heat-labile enterotoxin, a close relative of cholera toxin J. Mol. Biol. 230 1993 890 918
47. C.E. Bell, and D. Eisenberg Crystal structure of nucleotide-free diphtheria toxin Biochemistry 36 1997 481 488
48. M. Li, F. Dyda, I. Benhar, I. Pastan, and D.R. Davies Crystal structure of the catalytic domain of Pseudomonas exotoxin A complexed with a nicotinamide adenine dinucleotide analog: implications for the activation process and for ADP ribosylation Proc. Natl Acad. Sci. USA 93 1996 6902 6906
49. M. Li, F. Dyda, I. Benhar, I. Pastan, and D.R. Davies The crystal structure of Pseudomonas aeruginosa exotoxin domain III with nicotinamide and AMP: conformational differences with the intact exotoxin Proc. Natl Acad. Sci. USA 92 1995 9308 9312
50. J.E. Wedekind, C.B. Trame, M. Dorywalska, P. Koehl, T.M. Raschke, and M. McKee Refined crystallographic structure of Pseudomonas aeruginosa exotoxin A and its implications for the molecular mechanism of toxicity J. Mol. Biol. 314 2001 823 837
51. V.G. Johnson, and P.J. Nicholls Histidine 21 does not play a major role in diphtheria toxin catalysis J. Biol. Chem. 269 1994 4349 4354
52. S.R. Blanke, K. Huang, B.A. Wilson, E. Papini, A. Covacci, and R.J. Collier Active-site mutations of the diphtheria toxin catalytic domain: role of histidine-21 in nicotinamide adenine dinucleotide binding and ADP-ribosylation of elongation factor 2 Biochemistry 33 1994 5155 5161
53. E. Papini, G. Schiavo, R. Rappuoli, and C. Montecucco Histidine-21 is involved in diphtheria toxin NAD+ binding Toxicon 28 1990 631 635
54. B.A. Wilson, K.A. Reich, B.R. Weinstein, and R.J. Collier Active-site mutations of diphtheria toxin: effects of replacing glutamic acid-148 with aspartic acid, glutamine, or serine Biochemistry 29 1990 8643 8651
55. B.A. Wilson, and R.J. Collier Diphtheria toxin and Pseudomonas aeruginosa exotoxin A: active-site structure and enzymic mechanism Curr. Top. Microbiol. Immunol. 175 1992 27 41
56. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
57. T.C. Terwilliger, and J. Berendzen Automated MAD and MIR structure solution Acta Crystallog. sect. D 55 1999 849 861
58. 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
59. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, and R.W. Grosse-Kunstleve Crystallography and NMR system: a new software suite for macromolecular structure determination Acta Crystallog. sect. D 54 1998 905 921
60. 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
61. P.J. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 950 964
62. E.A. Merritt, and D.J. Bacon Raster3D: photorealistic molecular graphics Methods Enzymol. 277 1997 505 524
63. N.A. Baker, D. Sept, S. Joseph, M.J. Holst, and J.A. McCammon Electrostatics of nanosystems: application to microtubules and the ribosome Proc. Natl Acad. Sci. USA 98 2001 10037 10041
64. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucl. Acids Res. 22 1994 4673 4680
65. H. Shi, and P.B. Moore The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: a classic structure revisited RNA 6 2000 1091 1105