1e3p › Citations

A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation.

Symmons MF, Jones GH, Luisi BF
Structure 8 1215-26 (2000)
Cited: 154 times
EuropePMC logo PMID: 11080643

Abstract

Background

Polynucleotide phosphorylase (PNPase) is a polyribonucleotide nucleotidyl transferase (E.C.2.7.7.8) that degrades mRNA in prokaryotes. Streptomyces antibioticus PNPase also assays as a guanosine 3'-diphosphate 5'-triphosphate (pppGpp) synthetase (E.C.2.7.6.5). It may function to coordinate changes in mRNA lifetimes with pppGpp levels during the Streptomyces lifecycle.

Results

The structure of S. antibioticus PNPase without bound RNA but with the phosphate analog tungstate bound at the PNPase catalytic sites was determined by X-ray crystallography and shows a trimeric multidomain protein with a central channel. The structural core has a novel duplicated architecture formed by association of two homologous domains. The tungstate derivative structure reveals the PNPase active site in the second of these core domains. Structure-based sequence analysis suggests that the pppGpp synthetase active site is located in the first core domain.

Conclusion

This is the first structure of a PNPase and shows the structural basis for the trimer assembly, the arrangement of accessory RNA binding domains, and the likely catalytic residues of the PNPase active site. A possible function of the trimer channel is as a contribution to both the processivity of degradation and the regulation of PNPase action by RNA structural elements.

Reviews - 1e3p mentioned but not cited (5)

  1. The eukaryotic RNA exosome. Januszyk K, Lima CD. Curr Opin Struct Biol 24 132-140 (2014)
  2. Ro60 and Y RNAs: structure, functions, and roles in autoimmunity. Boccitto M, Wolin SL. Crit Rev Biochem Mol Biol 54 133-152 (2019)
  3. Structural components and architectures of RNA exosomes. Januszyk K, Lima CD. Adv Exp Med Biol 702 9-28 (2010)
  4. Information available at cut rates: structure and mechanism of ribonucleases. Worrall JA, Luisi BF. Curr Opin Struct Biol 17 128-137 (2007)
  5. Bacterial Y RNAs: Gates, Tethers, and tRNA Mimics. Sim S, Wolin SL. Microbiol Spectr 6 (2018)

Articles - 1e3p mentioned but not cited (9)

  1. Rules governing selective protein carbonylation. Maisonneuve E, Ducret A, Khoueiry P, Lignon S, Longhi S, Talla E, Dukan S. PLoS One 4 e7269 (2009)
  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. An RNA degradation machine sculpted by Ro autoantigen and noncoding RNA. Chen X, Taylor DW, Fowler CC, Galan JE, Wang HW, Wolin SL. Cell 153 166-177 (2013)
  4. Crystal structure of Escherichia coli PNPase: central channel residues are involved in processive RNA degradation. Shi Z, Yang WZ, Lin-Chao S, Chak KF, Yuan HS. RNA 14 2361-2371 (2008)
  5. A complex prediction: three-dimensional model of the yeast exosome. Aloy P, Ciccarelli FD, Leutwein C, Gavin AC, Superti-Furga G, Bork P, Bottcher B, Russell RB, Russell RB. EMBO Rep 3 628-635 (2002)
  6. Crystal structure of human polynucleotide phosphorylase: insights into its domain function in RNA binding and degradation. Lin CL, Wang YT, Yang WZ, Hsiao YY, Yuan HS. Nucleic Acids Res 40 4146-4157 (2012)
  7. A mutation in polynucleotide phosphorylase from Escherichia coli impairing RNA binding and degradosome stability. Regonesi ME, Briani F, Ghetta A, Zangrossi S, Ghisotti D, Tortora P, Dehò G. Nucleic Acids Res 32 1006-1017 (2004)
  8. Inhibition of homologous phosphorolytic ribonucleases by citrate may represent an evolutionarily conserved communicative link between RNA degradation and central metabolism. Stone CM, Butt LE, Bufton JC, Lourenco DC, Gowers DM, Pickford AR, Cox PA, Vincent HA, Callaghan AJ. Nucleic Acids Res 45 4655-4666 (2017)
  9. Sequence-structure mapping errors in the PDB: OB-fold domains. Venclovas C, Ginalski K, Kang C. Protein Sci 13 1594-1602 (2004)


Reviews citing this publication (38)

  1. The enzymes and control of eukaryotic mRNA turnover. Parker R, Song H. Nat Struct Mol Biol 11 121-127 (2004)
  2. The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Carpousis AJ. Annu Rev Microbiol 61 71-87 (2007)
  3. Messenger RNA turnover in eukaryotes: pathways and enzymes. Meyer S, Temme C, Wahle E. Crit Rev Biochem Mol Biol 39 197-216 (2004)
  4. The critical role of RNA processing and degradation in the control of gene expression. Arraiano CM, Andrade JM, Domingues S, Guinote IB, Malecki M, Matos RG, Moreira RN, Pobre V, Reis FP, Saramago M, Silva IJ, Viegas SC. FEMS Microbiol Rev 34 883-923 (2010)
  5. A structural perspective on protein-protein interactions. Russell RB, Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. Curr Opin Struct Biol 14 313-324 (2004)
  6. RNA decay machines: the exosome. Chlebowski A, Lubas M, Jensen TH, Dziembowski A. Biochim Biophys Acta 1829 552-560 (2013)
  7. A structural basis for processivity. Breyer WA, Matthews BW. Protein Sci 10 1699-1711 (2001)
  8. Messenger RNA degradation in bacterial cells. Hui MP, Foley PL, Belasco JG. Annu Rev Genet 48 537-559 (2014)
  9. The exosome and RNA quality control in the nucleus. Vanacova S, Stefl R. EMBO Rep 8 651-657 (2007)
  10. RNA remodeling and gene regulation by cold shock proteins. Phadtare S, Severinov K. RNA Biol 7 788-795 (2010)
  11. Bacterial ribonucleases and their roles in RNA metabolism. Bechhofer DH, Deutscher MP. Crit Rev Biochem Mol Biol 54 242-300 (2019)
  12. The exosome and the proteasome: nano-compartments for degradation. Lorentzen E, Conti E. Cell 125 651-654 (2006)
  13. From conformational chaos to robust regulation: the structure and function of the multi-enzyme RNA degradosome. Górna MW, Carpousis AJ, Luisi BF. Q Rev Biophys 45 105-145 (2012)
  14. The social fabric of the RNA degradosome. Bandyra KJ, Bouvier M, Carpousis AJ, Luisi BF. Biochim Biophys Acta 1829 514-522 (2013)
  15. Importance and key events of prokaryotic RNA decay: the ultimate fate of an RNA molecule. Silva IJ, Saramago M, Dressaire C, Domingues S, Viegas SC, Arraiano CM. Wiley Interdiscip Rev RNA 2 818-836 (2011)
  16. PNPASE and RNA trafficking into mitochondria. Wang G, Shimada E, Koehler CM, Teitell MA. Biochim Biophys Acta 1819 998-1007 (2012)
  17. The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines. Lin-Chao S, Chiou NT, Schuster G. J Biomed Sci 14 523-532 (2007)
  18. Intracellular ribonucleases involved in transcript processing and decay: precision tools for RNA. Arraiano CM, Mauxion F, Viegas SC, Matos RG, Séraphin B. Biochim Biophys Acta 1829 491-513 (2013)
  19. Human polynucleotide phosphorylase: location matters. Chen HW, Koehler CM, Teitell MA. Trends Cell Biol 17 600-608 (2007)
  20. Polynucleotide phosphorylase: an evolutionary conserved gene with an expanding repertoire of functions. Sarkar D, Fisher PB. Pharmacol Ther 112 243-263 (2006)
  21. Structural organization of the RNA-degrading exosome. Lorentzen E, Basquin J, Conti E. Curr Opin Struct Biol 18 709-713 (2008)
  22. The exosome: a macromolecular cage for controlled RNA degradation. Büttner K, Wenig K, Hopfner KP. Mol Microbiol 61 1372-1379 (2006)
  23. Mechanisms of RNA degradation by the eukaryotic exosome. Tomecki R, Tomecki R, Drazkowska K, Dziembowski A. Chembiochem 11 938-945 (2010)
  24. Battle against RNA oxidation: molecular mechanisms for reducing oxidized RNA to protect cells. Li Z, Malla S, Shin B, Li JM. Wiley Interdiscip Rev RNA 5 335-346 (2014)
  25. Regulation and functions of bacterial PNPase. Briani F, Carzaniga T, Dehò G. Wiley Interdiscip Rev RNA 7 241-258 (2016)
  26. Exosome substrate targeting: the long and short of it. Mitchell P. Biochem Soc Trans 42 1129-1134 (2014)
  27. Rarely at rest: RNA helicases and their busy contributions to RNA degradation, regulation and quality control. Hardwick SW, Luisi BF. RNA Biol 10 56-70 (2013)
  28. Polynucleotide phosphorylase: Not merely an RNase but a pivotal post-transcriptional regulator. Cameron TA, Matz LM, De Lay NR. PLoS Genet 14 e1007654 (2018)
  29. Human polynucleotide phosphorylase (hPNPase(old-35)): an evolutionary conserved gene with an expanding repertoire of RNA degradation functions. Das SK, Bhutia SK, Sokhi UK, Dash R, Azab B, Sarkar D, Fisher PB. Oncogene 30 1733-1743 (2011)
  30. Structure and function of the archaeal exosome. Evguenieva-Hackenberg E, Hou L, Glaeser S, Klug G. Wiley Interdiscip Rev RNA 5 623-635 (2014)
  31. The exoribonuclease Polynucleotide Phosphorylase influences the virulence and stress responses of yersiniae and many other pathogens. Rosenzweig JA, Chopra AK. Front Cell Infect Microbiol 3 81 (2013)
  32. Exonucleases and endonucleases involved in polyadenylation-assisted RNA decay. Slomovic S, Schuster G. Wiley Interdiscip Rev RNA 2 106-123 (2011)
  33. Activity and Function in Human Cells of the Evolutionary Conserved Exonuclease Polynucleotide Phosphorylase. Falchi FA, Pizzoccheri R, Briani F. Int J Mol Sci 23 1652 (2022)
  34. Novel Aspects of Polynucleotide Phosphorylase Function in Streptomyces. Jones GH. Antibiotics (Basel) 7 E25 (2018)
  35. The Bacterial Counterparts of the Eukaryotic Exosome: An Evolutionary Perspective. Viegas SC, Matos RG, Arraiano CM. Methods Mol Biol 2062 37-46 (2020)
  36. Streptomyces RNases - Function and impact on antibiotic synthesis. Jones GH. Front Microbiol 14 1096228 (2023)
  37. Methodologies for bacterial ribonuclease characterization using RNA-seq. Broglia L, Le Rhun A, Charpentier E. FEMS Microbiol Rev 47 fuad049 (2023)
  38. Strategies for Generating RNA Exosome Complexes from Recombinant Expression Hosts. Weick EM, Zinder JC, Lima CD. Methods Mol Biol 2062 417-425 (2020)

Articles citing this publication (102)

  1. Reconstitution, activities, and structure of the eukaryotic RNA exosome. Liu Q, Greimann JC, Lima CD. Cell 127 1223-1237 (2006)
  2. A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Dziembowski A, Lorentzen E, Conti E, Séraphin B. Nat Struct Mol Biol 14 15-22 (2007)
  3. PNPASE regulates RNA import into mitochondria. Wang G, Chen HW, Oktay Y, Zhang J, Allen EL, Smith GM, Fan KC, Hong JS, French SW, McCaffery JM, Lightowlers RN, Morse HC, Koehler CM, Teitell MA. Cell 142 456-467 (2010)
  4. The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities. Schaeffer D, Tsanova B, Barbas A, Reis FP, Dastidar EG, Sanchez-Rotunno M, Arraiano CM, van Hoof A. Nat Struct Mol Biol 16 56-62 (2009)
  5. The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation. Bonneau F, Basquin J, Ebert J, Lorentzen E, Conti E. Cell 139 547-559 (2009)
  6. The N-terminal PIN domain of the exosome subunit Rrp44 harbors endonuclease activity and tethers Rrp44 to the yeast core exosome. Schneider C, Leung E, Brown J, Tollervey D. Nucleic Acids Res 37 1127-1140 (2009)
  7. 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)
  8. Structural framework for the mechanism of archaeal exosomes in RNA processing. Büttner K, Wenig K, Hopfner KP. Mol Cell 20 461-471 (2005)
  9. Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E. Callaghan AJ, Aurikko JP, Ilag LL, Günter Grossmann J, Chandran V, Kühnel K, Poljak L, Carpousis AJ, Robinson CV, Symmons MF, Luisi BF. J Mol Biol 340 965-979 (2004)
  10. Human mitochondrial RNA decay mediated by PNPase-hSuv3 complex takes place in distinct foci. Borowski LS, Dziembowski A, Hejnowicz MS, Stepien PP, Szczesny RJ. Nucleic Acids Res 41 1223-1240 (2013)
  11. Mammalian polynucleotide phosphorylase is an intermembrane space RNase that maintains mitochondrial homeostasis. Chen HW, Rainey RN, Balatoni CE, Dawson DW, Troke JJ, Wasiak S, Hong JS, McBride HM, Koehler CM, Teitell MA, French SW. Mol Cell Biol 26 8475-8487 (2006)
  12. Polynucleotide phosphorylase functions as both an exonuclease and a poly(A) polymerase in spinach chloroplasts. Yehudai-Resheff S, Hirsh M, Schuster G. Mol Cell Biol 21 5408-5416 (2001)
  13. Mutations in DNA methyltransferase (DNMT3A) observed in acute myeloid leukemia patients disrupt processive methylation. Holz-Schietinger C, Matje DM, Reich NO. J Biol Chem 287 30941-30951 (2012)
  14. Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core. Lorentzen E, Conti E. Mol Cell 20 473-481 (2005)
  15. Exo- and endoribonucleolytic activities of yeast cytoplasmic and nuclear RNA exosomes are dependent on the noncatalytic core and central channel. Wasmuth EV, Lima CD. Mol Cell 48 133-144 (2012)
  16. PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader. Jarrige AC, Mathy N, Portier C. EMBO J 20 6845-6855 (2001)
  17. The RNA degradosome: life in the fast lane of adaptive molecular evolution. Marcaida MJ, DePristo MA, Chandran V, Carpousis AJ, Luisi BF. Trends Biochem Sci 31 359-365 (2006)
  18. A new function in translocation for the mitochondrial i-AAA protease Yme1: import of polynucleotide phosphorylase into the intermembrane space. Rainey RN, Glavin JD, Chen HW, French SW, Teitell MA, Koehler CM. Mol Cell Biol 26 8488-8497 (2006)
  19. Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring. Raijmakers R, Egberts WV, van Venrooij WJ, Pruijn GJ. J Mol Biol 323 653-663 (2002)
  20. Mutational analysis of the SARS virus Nsp15 endoribonuclease: identification of residues affecting hexamer formation. Guarino LA, Bhardwaj K, Dong W, Sun J, Holzenburg A, Kao C. J Mol Biol 353 1106-1117 (2005)
  21. Structural basis for processivity and single-strand specificity of RNase II. Zuo Y, Vincent HA, Zhang J, Wang Y, Deutscher MP, Malhotra A. Mol Cell 24 149-156 (2006)
  22. The PMC2NT domain of the catalytic exosome subunit Rrp6p provides the interface for binding with its cofactor Rrp47p, a nucleic acid-binding protein. Stead JA, Costello JL, Livingstone MJ, Mitchell P. Nucleic Acids Res 35 5556-5567 (2007)
  23. Reconstitution and analysis of the multienzyme Escherichia coli RNA degradosome. Worrall JA, Górna M, Crump NT, Phillips LG, Tuck AC, Price AJ, Bavro VN, Luisi BF. J Mol Biol 382 870-883 (2008)
  24. Mutational analysis of polynucleotide phosphorylase from Escherichia coli. Jarrige A, Bréchemier-Baey D, Mathy N, Duché O, Portier C. J Mol Biol 321 397-409 (2002)
  25. Chloroplast PNPase exists as a homo-multimer enzyme complex that is distinct from the Escherichia coli degradosome. Baginsky S, Shteiman-Kotler A, Liveanu V, Yehudai-Resheff S, Bellaoui M, Settlage RE, Shabanowitz J, Hunt DF, Schuster G, Gruissem W. RNA 7 1464-1475 (2001)
  26. Activities of human RRP6 and structure of the human RRP6 catalytic domain. Januszyk K, Liu Q, Lima CD. RNA 17 1566-1577 (2011)
  27. Modulation of yersinia type three secretion system by the S1 domain of polynucleotide phosphorylase. Rosenzweig JA, Weltman G, Plano GV, Schesser K. J Biol Chem 280 156-163 (2005)
  28. Polynucleotide phosphorylase negatively controls spv virulence gene expression in Salmonella enterica. Ygberg SE, Clements MO, Rytkönen A, Thompson A, Holden DW, Hinton JC, Rhen M. Infect Immun 74 1243-1254 (2006)
  29. Domain analysis of the chloroplast polynucleotide phosphorylase reveals discrete functions in RNA degradation, polyadenylation, and sequence homology with exosome proteins. Yehudai-Resheff S, Portnoy V, Yogev S, Adir N, Schuster G. Plant Cell 15 2003-2019 (2003)
  30. Oligomerization of DNMT3A controls the mechanism of de novo DNA methylation. Holz-Schietinger C, Matje DM, Harrison MF, Reich NO. J Biol Chem 286 41479-41488 (2011)
  31. The origin of polynucleotide phosphorylase domains. Leszczyniecka M, DeSalle R, Kang DC, Fisher PB. Mol Phylogenet Evol 31 123-130 (2004)
  32. Polynucleotide phosphorylase activity may be modulated by metabolites in Escherichia coli. Nurmohamed S, Vincent HA, Titman CM, Chandran V, Pears MR, Du D, Griffin JL, Callaghan AJ, Luisi BF. J Biol Chem 286 14315-14323 (2011)
  33. Crystal structure of Caulobacter crescentus polynucleotide phosphorylase reveals a mechanism of RNA substrate channelling and RNA degradosome assembly. Hardwick SW, Gubbey T, Hug I, Jenal U, Luisi BF. Open Biol 2 120028 (2012)
  34. Defining the domains of human polynucleotide phosphorylase (hPNPaseOLD-35) mediating cellular senescence. Sarkar D, Park ES, Emdad L, Randolph A, Valerie K, Fisher PB. Mol Cell Biol 25 7333-7343 (2005)
  35. Insights into the mechanism of progressive RNA degradation by the archaeal exosome. Navarro MV, Oliveira CC, Zanchin NI, Guimarães BG. J Biol Chem 283 14120-14131 (2008)
  36. Stimulation of poly(A) synthesis by Escherichia coli poly(A)polymerase I is correlated with Hfq binding to poly(A) tails. Folichon M, Allemand F, Régnier P, Hajnsdorf E. FEBS J 272 454-463 (2005)
  37. Characterization of native and reconstituted exosome complexes from the hyperthermophilic archaeon Sulfolobus solfataricus. Walter P, Klein F, Lorentzen E, Ilchmann A, Klug G, Evguenieva-Hackenberg E. Mol Microbiol 62 1076-1089 (2006)
  38. Analysis of the human polynucleotide phosphorylase (PNPase) reveals differences in RNA binding and response to phosphate compared to its bacterial and chloroplast counterparts. Portnoy V, Palnizky G, Yehudai-Resheff S, Glaser F, Schuster G. RNA 14 297-309 (2008)
  39. Mutational analysis of Arabidopsis chloroplast polynucleotide phosphorylase reveals roles for both RNase PH core domains in polyadenylation, RNA 3'-end maturation and intron degradation. Germain A, Herlich S, Larom S, Kim SH, Schuster G, Stern DB. Plant J 67 381-394 (2011)
  40. The ribonuclease polynucleotide phosphorylase can interact with small regulatory RNAs in both protective and degradative modes. Bandyra KJ, Sinha D, Syrjanen J, Luisi BF, De Lay NR. RNA 22 360-372 (2016)
  41. Antisense transcript and RNA processing alterations suppress instability of polyadenylated mRNA in chlamydomonas chloroplasts. Nishimura Y, Kikis EA, Zimmer SL, Komine Y, Stern DB. Plant Cell 16 2849-2869 (2004)
  42. RNase activity of polynucleotide phosphorylase is critical at low temperature in Escherichia coli and is complemented by RNase II. Awano N, Inouye M, Phadtare S. J Bacteriol 190 5924-5933 (2008)
  43. Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus. Ishii R, Nureki O, Yokoyama S. J Biol Chem 278 32397-32404 (2003)
  44. (p)ppGpp inhibits polynucleotide phosphorylase from streptomyces but not from Escherichia coli and increases the stability of bulk mRNA in Streptomyces coelicolor. Gatewood ML, Jones GH. J Bacteriol 192 4275-4280 (2010)
  45. Polynucleotide Phosphorylase Regulates Multiple Virulence Factors and the Stabilities of Small RNAs RsmY/Z in Pseudomonas aeruginosa. Chen R, Weng Y, Zhu F, Jin Y, Liu C, Pan X, Xia B, Cheng Z, Jin S, Wu W. Front Microbiol 7 247 (2016)
  46. 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)
  47. Reconstitution of RNA exosomes from human and Saccharomyces cerevisiae cloning, expression, purification, and activity assays. Greimann JC, Lima CD. Methods Enzymol 448 185-210 (2008)
  48. RNA degradation by the plant RNA exosome involves both phosphorolytic and hydrolytic activities. Sikorska N, Zuber H, Gobert A, Lange H, Gagliardi D. Nat Commun 8 2162 (2017)
  49. S1 and KH domains of polynucleotide phosphorylase determine the efficiency of RNA binding and autoregulation. Wong AG, McBurney KL, Thompson KJ, Stickney LM, Mackie GA. J Bacteriol 195 2021-2031 (2013)
  50. The TCL1 oncoprotein binds the RNase PH domains of the PNPase exoribonuclease without affecting its RNA degrading activity. French SW, Dawson DW, Chen HW, Rainey RN, Sievers SA, Balatoni CE, Wong L, Troke JJ, Nguyen MT, Koehler CM, Teitell MA. Cancer Lett 248 198-210 (2007)
  51. Crystal structure of imidazole glycerol-phosphate dehydratase: duplication of an unusual fold. Sinha SC, Chaudhuri BN, Burgner JW, Yakovleva G, Davisson VJ, Smith JL. J Biol Chem 279 15491-15498 (2004)
  52. 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)
  53. The X-ray structure of Escherichia coli RraA (MenG), A protein inhibitor of RNA processing. Monzingo AF, Gao J, Qiu J, Georgiou G, Robertus JD. J Mol Biol 332 1015-1024 (2003)
  54. When ribonucleases come into play in pathogens: a survey of gram-positive bacteria. Jester BC, Romby P, Lioliou E. Int J Microbiol 2012 592196 (2012)
  55. Interaction of Bacillus subtilis Polynucleotide Phosphorylase and RNase Y: STRUCTURAL MAPPING AND EFFECT ON mRNA TURNOVER. Salvo E, Alabi S, Liu B, Schlessinger A, Bechhofer DH. J Biol Chem 291 6655-6663 (2016)
  56. Novel CalphaNN structural motif for protein recognition of phosphate ions. Denessiouk KA, Johnson MS, Denesyuk AI. J Mol Biol 345 611-629 (2005)
  57. The evolutionarily conserved subunits Rrp4 and Csl4 confer different substrate specificities to the archaeal exosome. Roppelt V, Klug G, Evguenieva-Hackenberg E. FEBS Lett 584 2931-2936 (2010)
  58. Genome-based analysis of Chlamydomonas reinhardtii exoribonucleases and poly(A) polymerases predicts unexpected organellar and exosomal features. Zimmer SL, Fei Z, Stern DB. Genetics 179 125-136 (2008)
  59. Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring. Lu C, Ding F, Ke A. PLoS One 5 e8739 (2010)
  60. Comment Doughnuts dealing with RNA. Pruijn GJ. Nat Struct Mol Biol 12 562-564 (2005)
  61. Nucleic acid and protein factors involved in Escherichia coli polynucleotide phosphorylase function on RNA. Fernández-Ramírez F, Bermúdez-Cruz RM, Bermúdez-Cruz RM, Montañez C. Biochimie 92 445-454 (2010)
  62. Structure and Activities of the Eukaryotic RNA Exosome. Wasmuth EV, Lima CD. Enzymes 31 53-75 (2012)
  63. Crystal structure of a 9-subunit archaeal exosome in pre-catalytic states of the phosphorolytic reaction. Lorentzen E, Conti E. Archaea 2012 721869 (2012)
  64. Direct observation of processive exoribonuclease motion using optical tweezers. Fazal FM, Koslover DJ, Luisi BF, Block SM. Proc Natl Acad Sci U S A 112 15101-15106 (2015)
  65. Overexpression and purification of untagged polynucleotide phosphorylases. Jones GH, Symmons MF, Hankins JS, Mackie GA. Protein Expr Purif 32 202-209 (2003)
  66. Structural Insights into a Unique Dimeric DEAD-Box Helicase CshA that Promotes RNA Decay. Huen J, Lin CL, Golzarroshan B, Yi WL, Yang WZ, Yuan HS. Structure 25 469-481 (2017)
  67. Kinetics of polynucleotide phosphorylase: comparison of enzymes from Streptomyces and Escherichia coli and effects of nucleoside diphosphates. Chang SA, Cozad M, Mackie GA, Jones GH. J Bacteriol 190 98-106 (2008)
  68. A conserved loop in polynucleotide phosphorylase (PNPase) essential for both RNA and ADP/phosphate binding. Carzaniga T, Mazzantini E, Nardini M, Regonesi ME, Greco C, Briani F, De Gioia L, Dehò G, Tortora P. Biochimie 97 49-59 (2014)
  69. Archaeal DnaG contains a conserved N-terminal RNA-binding domain and enables tailing of rRNA by the exosome. Hou L, Klug G, Evguenieva-Hackenberg E. Nucleic Acids Res 42 12691-12706 (2014)
  70. Distinctive effects of domain deletions on the manganese-dependent DNA polymerase and DNA phosphorylase activities of Mycobacterium smegmatis polynucleotide phosphorylase. Unciuleac MC, Shuman S. Biochemistry 52 2967-2981 (2013)
  71. Polynucleotide phosphorylase binds to ssRNA with same affinity as to ssDNA. Bermúdez-Cruz RM, Bermúdez-Cruz RM, García-Mena J, Montañez C. Biochimie 84 321-328 (2002)
  72. A blue native-PAGE analysis of membrane protein complexes in Clostridium thermocellum. Peng Y, Luo Y, Yu T, Xu X, Fan K, Zhao Y, Yang K. BMC Microbiol 11 22 (2011)
  73. From polynucleotide phosphorylase to neurobiology. Littauer UZ. J Biol Chem 280 38889-38897 (2005)
  74. 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)
  75. 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)
  76. PNPase knockout results in mtDNA loss and an altered metabolic gene expression program. Shimada E, Ahsan FM, Nili M, Huang D, Atamdede S, TeSlaa T, Case D, Yu X, Gregory BD, Perrin BJ, Koehler CM, Teitell MA. PLoS One 13 e0200925 (2018)
  77. Polynucleotide phosphorylase is implicated in homologous recombination and DNA repair in Escherichia coli. Carzaniga T, Sbarufatti G, Briani F, Dehò G. BMC Microbiol 17 81 (2017)
  78. Transient expression of βC1 protein differentially regulates host genes related to stress response, chloroplast and mitochondrial functions. Andleeb S, Amin I, Bashir A, Briddon RW, Mansoor S. Virol J 7 373 (2010)
  79. Discrimination of RNA from DNA by polynucleotide phosphorylase. Unciuleac MC, Shuman S. Biochemistry 52 6702-6711 (2013)
  80. 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)
  81. Quantitative analysis of cellular proteome alterations of Pseudomonas putida to naphthalene-induced stress. Li SS, Hu X, Zhao H, Li YX, Zhang L, Gong LJ, Guo J, Zhao HB. Biotechnol Lett 37 1645-1654 (2015)
  82. Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement. Makino DL, Conti E. Acta Crystallogr D Biol Crystallogr 69 2226-2235 (2013)
  83. 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)
  84. The effects of RNA degradation enzymes on antisense RNAI controlling ColE2 plasmid copy number. Nishio SY, Itoh T. Plasmid 60 174-180 (2008)
  85. Polynucleotide phosphorylase and RNA helicase CshA cooperate in Bacillus subtilis mRNA decay. Ingle S, Chhabra S, Laspina D, Salvo E, Liu B, Bechhofer DH. RNA Biol 18 1692-1701 (2021)
  86. Structure and mechanism of Mycobacterium smegmatis polynucleotide phosphorylase. Unciuleac MC, Ghosh S, de la Cruz MJ, Goldgur Y, Shuman S. RNA rna.078822.121 (2021)
  87. Characterization of the Catalytic Subunits of the RNA Exosome-like Complex in Plasmodium falciparum. Jiang N, Yu S, Yang N, Feng Y, Sang X, Wang Y, Wahlgren M, Chen Q. J Eukaryot Microbiol 65 843-853 (2018)
  88. Critical roles for 'housekeeping' nucleases in type III CRISPR-Cas immunity. Chou-Zheng L, Hatoum-Aslan A. Elife 11 e81897 (2022)
  89. Crystallization and preliminary X-ray diffraction studies of Xanthomonas campestris PNPase in the presence of c-di-GMP. Wang YC, Chin KH, Chuah ML, Liang ZX, Chou SH. Acta Crystallogr Sect F Struct Biol Cryst Commun 68 1247-1250 (2012)
  90. Factors influencing RNA degradation by Thermus thermophilus polynucleotide phosphorylase. Falaleeva MV, Chetverina HV, Ugarov VI, Uzlova EA, Chetverin AB. FEBS J 275 2214-2226 (2008)
  91. Functions of Conserved Domains of Human Polynucleotide Phosphorylase on RNA Oxidation. Malla S, Li Z. Insights Biomed Res 3 62-67 (2019)
  92. Streptomyces coelicolor polynucleotide phosphorylase can polymerize nucleoside diphosphates under phosphorolysis conditions, with implications for the degradation of structured RNAs. Jones GH, Mackie GA. J Bacteriol 195 5151-5159 (2013)
  93. Comment Wrong PH for RNA degradation. Wahle E. Nat Struct Mol Biol 14 5-7 (2007)
  94. Polymer phosphorylases: clues to the emergence of non-replicative and replicative polymers. Freire MA. Theory Biosci 130 279-287 (2011)
  95. Pseudomonas aeruginosa Polynucleotide Phosphorylase Controls Tolerance to Aminoglycoside Antibiotics by Regulating the MexXY Multidrug Efflux Pump. Fan Z, Pan X, Wang D, Chen R, Fu T, Yang B, Jin Y, Bai F, Cheng Z, Wu W. Antimicrob Agents Chemother 65 e01846-20 (2021)
  96. Anion induced conformational preference of Cα NN motif residues in functional proteins. Patra P, Ghosh M, Banerjee R, Chakrabarti J. Proteins 85 2179-2190 (2017)
  97. Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi. Petroni E, Esnault C, Tetreault D, Dale RK, Storz G, Adams PP. Nat Commun 14 3931 (2023)
  98. Poring over exosome structure. Tsanova B, van Hoof A. EMBO Rep 11 900-901 (2010)
  99. iCLIP analysis of RNA substrates of the archaeal exosome. Bathke J, Gauernack AS, Rupp O, Weber L, Preusser C, Lechner M, Rossbach O, Goesmann A, Evguenieva-Hackenberg E, Klug G. BMC Genomics 21 797 (2020)
  100. Quantum chemical studies on anion specificity of CαNN motif in functional proteins. Patra P, Ghosh M, Banerjee R, Chakrabarti J. J Comput Aided Mol Des 32 929-936 (2018)
  101. 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)
  102. β-Strand-mediated interactions of protein domains. Bhat AS, Kinch LN, Grishin NV. Proteins 88 1513-1527 (2020)


Quick links