Crystal structure of a 9-subunit archaeal exosome in pre-catalytic states of the phosphorolytic reaction

Archaea

Volumn 2012, Issue , 2012, Pages

  Lorentzen, Esben ^a   Conti, Elena ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

ARCHAEAL PROTEIN; ARCHAEAL RNA; EXOSOME MULTIENZYME RIBONUCLEASE COMPLEX; PHOSPHATE; POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME ACTIVE SITE; ENZYMOLOGY; METABOLISM; PROTEIN SUBUNIT; RNA PROCESSING; SULFOLOBUS SOLFATARICUS; X RAY CRYSTALLOGRAPHY;

ARCHAEAL PROTEINS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; EXOSOME MULTIENZYME RIBONUCLEASE COMPLEX; MODELS, MOLECULAR; PHOSPHATES; POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE; PROTEIN SUBUNITS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, ARCHAEAL; SULFOLOBUS SOLFATARICUS;

MLCS; MLOWN;

EID: 84872131987     PISSN: 14723646     EISSN: None     Source Type: Journal    
DOI: 10.1155/2012/721869     Document Type: Article

References (33)

1. Houseley J., LaCava J., Tollervey D., RNA-quality control by the exosome. Nature Reviews Molecular Cell Biology 2006 7 7 529 539 2-s2.0-33745869788 10.1038/nrm1964 (Pubitemid 44036458)
2. Lorentzen E., Conti E., The exosome and the proteasome: nano-compartments for degradation. Cell 2006 125 4 651 654 2-s2.0-33646523370 10.1016/j.cell.2006.05.002
3. Büttner K., Wenig K., Hopfner K. P., Structural framework for the mechanism of archaeal exosomes in RNA processing. Molecular Cell 2005 20 3 461 471 2-s2.0-27644435644 10.1016/j.molcel.2005.10.018 (Pubitemid 41572302)
4. Lorentzen E., Dziembowski A., Lindner D., Seraphin B., Conti E., RNA channelling by the archaeal exosome. EMBO Reports 2007 8 5 470 476 2-s2.0-34247844604 10.1038/sj.embor.7400945 (Pubitemid 46696517)
5. Bonneau F., Basquin J., Ebert J., Lorentzen E., Conti E., The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation. Cell 2009 139 3 547 559 2-s2.0-70350336247 10.1016/j.cell.2009.08. 042
6. Malet H., Topf M., Clare D. K., Ebert J., Bonneau F., Basquin J., Drazkowska K., Tomecki R., Dziembowski A., Conti E., Saibil H. R., Lorentzen E., RNA channelling by the eukaryotic exosome. EMBO Reports 2010 11 12 936 942 2-s2.0-78649469070 10.1038/embor.2010.164
7. Wasmuth E. V., Lima C. D., Exo- and endoribonucleolytic activities of yeast cytoplasmic and nuclear RNA exosomes are dependent on the noncatalytic core and central channel. Molecular Cell 2012 48 1 133 144
8. Liu Q., Greimann J. C., Lima C. D., Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 2006 127 6 1223 1237 2-s2.0-33845407784 10.1016/j.cell.2006.10.037 (Pubitemid 44894519)
9. Dziembowski A., Lorentzen E., Conti E., Séraphin B., A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nature Structural and Molecular Biology 2007 14 1 15 22 2-s2.0-33846068920 10.1038/nsmb1184 (Pubitemid 46067418)
10. Lorentzen E., Walter P., Fribourg S., Evguenieva-Hackenberg E., Klug G., Conti E., The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nature Structural and Molecular Biology 2005 12 7 575 581 2-s2.0-22144493835 10.1038/nsmb952 (Pubitemid 40980806)
11. Walter P., Klein F., Lorentzen E., Ilchmann A., Klug G., Evguenieva-Hackenberg E., Characterization of native and reconstituted exosome complexes from the hyperthermophilic archaeon Sulfolobus solfataricus. Molecular Microbiology 2006 62 4 1076 1089 2-s2.0-33750440205 10.1111/j.1365-2958.2006. 05393.x (Pubitemid 44655319)
12. Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D., Mitchell P., The yeast exosome and human PM-Scl are related complexes of 3′ → 5′ exonucleases. Genes and Development 1999 13 16 2148 2158 2-s2.0-0033567131 (Pubitemid 29407354)
13. Mitchell P., Petfalski E., Shevchenko A., Mann M., Tollervey D., The exosome: a conserved eukaryotic RNA processing complex containing multiple 3′ → 5′ exoribonucleases. Cell 1997 91 4 457 466 2-s2.0-0030702085 (Pubitemid 27508235)
14. Lorentzen E., Basquin J., Tomecki R., Dziembowski A., Conti E., Structure of the active subunit of the yeast exosome core, Rrp44: diverse modes of substrate recruitment in the RNase II nuclease family. Molecular Cell 2008 29 6 717 728 2-s2.0-40849106786 10.1016/j.molcel.2008.02.018 (Pubitemid 351400929)
15. Allmang C., Kufel J., Chanfreau G., Mitchell P., Petfalski E., Tollervey D., Functions of the exosome in rRNA, snoRNA and snRNA synthesis. The EMBO Journal 1999 18 19 5399 5410 2-s2.0-0033214175 10.1093/emboj/18.19.5399 (Pubitemid 29465589)
16. Midtgaard S. F., Assenholt J., Jonstrup A. T., Van L. B., Jensen T. H., Brodersen D. E., Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain. Proceedings of the National Academy of Sciences of the United States of America 2006 103 32 11898 11903 2-s2.0-33747041640 10.1073/pnas.0604731103 (Pubitemid 44215783)
17. Stead J. A., Costello J. L., Livingstone M. J., Mitchell P., The PMC2NT domain of the catalytic exosome subunit Rrp6p provides the interface for binding with its cofactor Rrp47p, a nucleic acid-binding protein. Nucleic Acids Research 2007 35 16 5556 5567 2-s2.0-34548712987 10.1093/nar/gkm614 (Pubitemid 47430457)
18. Portnoy V., Evguenieva-Hackenberg E., Klein F., Walter P., Lorentzen E., Klug G., Schuster G., RNA polyadenylation in archaea: not observed in Haloferax while the exosome polynucleotidylates RNA in Sulfolobus. EMBO Reports 2005 6 12 1188 1193 2-s2.0-28544443737 10.1038/sj.embor.7400571 (Pubitemid 41741704)
19. Portnoy V., Schuster G., RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R. Nucleic Acids Research 2006 34 20 5923 5931 2-s2.0-33845606715 10.1093/nar/gkl763 (Pubitemid 44941171)
20. Symmons M. F., Jones G. H., Luisi B. F., A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation. Structure 2000 8 11 1215 1226 2-s2.0-0034435974 10.1016/S0969-2126(00)00521-9 (Pubitemid 32667486)
21. Symmons M. F., Williams M. G., Luisi B. F., Jones G. H., Carpousis A. J., Running rings around RNA: a superfamily of phosphate-dependent RNases. Trends in Biochemical Sciences 2002 27 1 11 18 2-s2.0-0036164937 10.1016/S0968-0004(01) 01999-5 (Pubitemid 34131620)
22. Lorentzen E., Conti E., Structural basis of 3′ end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core. Molecular Cell 2005 20 3 473 481 2-s2.0-27644496002 10.1016/j.molcel.2005.10.020 (Pubitemid 41572303)
23. Lu C., Ding F., Ke A., Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring. PLoS One 2010 5 1 2-s2.0-77649312626 10.1371/journal.pone.0008739 e8739
24. Navarro M. V. A. S., Oliveira C. C., Zanchin N. I. T., Guimarães B. G., Insights into the mechanism of progressive RNA degradation by the archaeal exosome. Journal of Biological Chemistry 2008 283 20 14120 14131 2-s2.0-46649091980 10.1074/jbc.M801005200
25. Ng C. L., Waterman D. G., Antson A. A., Ortiz-Lombardía M., Structure of the Methanothermobacter thermautotrophicus exosome RNase PH ring. Acta Crystallographica Section D 2010 66, part 5 522 528 2-s2.0-77952067132 10.1107/S0907444910002908
26. Evguenieva-Hackenberg E., Roppelt V., Finsterseifer P., Klug G., Rrp4 and Csl4 are needed for efficient degradation but not for polyadenylation of synthetic and natural RNA by the archaeal exosome. Biochemistry 2008 47 50 13158 13168 2-s2.0-57649134964 10.1021/bi8012214
27. Lorentzen E., Conti E., Expression, reconstitution, and structure of an archaeal RNA degrading exosome. Methods in Enzymology 2008 447 417 435 2-s2.0-58249083780 10.1016/S0076-6879(08)02220-9
28. Kabsch W., XDS. Acta Crystallogr D 2010 66, part 2 125 132
29. Murshudov G. N., Vagin A. A., Dodson E. J., Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallographica D 1997 53 3 240 255 2-s2.0-0030924992 10.1107/S0907444996012255 (Pubitemid 27235885)
30. Adams P. D., Afonine P. V., Bunkóczi G., PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D 2010 66, part 2 213 221
31. Emsley P., Lohkamp B., Scott W. G., Cowtan K., Features and development of Coot. Acta Crystallographica Section D 2010 66, part 4 486 501 2-s2.0-77949535720 10.1107/S0907444910007493
32. Harlow L. S., Kadziola A., Jensen K. F., Larsen S., Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding. Protein Science 2004 13 3 668 677 2-s2.0-1342331853 10.1110/ps.03477004 (Pubitemid 38252564)
33. Nurmohamed S., Vaidialingam B., Callaghan A. J., Luisi B. F., Crystal structure of escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly. Journal of Molecular Biology 2009 389 1 17 33 2-s2.0-67349257830 10.1016/j.jmb.2009.03.051