Item request has been placed! ×
Item request cannot be made. ×
loading  Processing Request

Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF.

Item request has been placed! ×
Item request cannot be made. ×
loading   Processing Request
اقرأ على الانترنت اقرأ أكثر حفظ في قائمتي
  • معلومة اضافية
    • المصدر:
      Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res
    • بيانات النشر:
      Publication: 1992- : Oxford : Oxford University Press
      Original Publication: London, Information Retrieval ltd.
    • الموضوع:
      Acid Anhydride Hydrolases/*chemistry ; Acid Anhydride Hydrolases/*metabolism ; Amino Acid Isomerases/*chemistry ; Escherichia coli Proteins/*chemistry ; Escherichia coli Proteins/*metabolism ; RNA, Messenger/*metabolism; Allosteric Regulation ; Amino Acid Isomerases/metabolism ; Kinetics ; Models, Molecular ; Protein Binding ; Protein Multimerization
    • نبذة مختصرة :
      Vitally important for controlling gene expression in eukaryotes and prokaryotes, the deprotection of mRNA 5' termini is governed by enzymes whose activity is modulated by interactions with ancillary factors. In Escherichia coli, 5'-end-dependent mRNA degradation begins with the generation of monophosphorylated 5' termini by the RNA pyrophosphohydrolase RppH, which can be stimulated by DapF, a diaminopimelate epimerase involved in amino acid and cell wall biosynthesis. We have determined crystal structures of RppH-DapF complexes and measured rates of RNA deprotection. These studies show that DapF potentiates RppH activity in two ways, depending on the nature of the substrate. Its stimulatory effect on the reactivity of diphosphorylated RNAs, the predominant natural substrates of RppH, requires a substrate long enough to reach DapF in the complex, while the enhanced reactivity of triphosphorylated RNAs appears to involve DapF-induced changes in RppH itself and likewise increases with substrate length. This study provides a basis for understanding the intricate relationship between cellular metabolism and mRNA decay and reveals striking parallels with the stimulation of decapping activity in eukaryotes.
    • References:
      J Bacteriol. 2012 Nov;194(22):6233-9. (PMID: 22984254)
      J Biol Chem. 2013 Mar 29;288(13):9238-48. (PMID: 23426375)
      Science. 2012 Dec 7;338(6112):1344-8. (PMID: 23224554)
      Mol Cell. 2011 Sep 16;43(6):940-9. (PMID: 21925382)
      Genes Dev. 2013 Dec 15;27(24):2628-41. (PMID: 24352420)
      Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501. (PMID: 20383002)
      Nat Rev Mol Cell Biol. 2010 Jul;11(7):467-78. (PMID: 20520623)
      Gene. 1998 Jan 30;207(2):149-57. (PMID: 9511756)
      J Bacteriol. 2007 May;189(9):3434-44. (PMID: 17337586)
      Mol Microbiol. 2000 Apr;36(1):174-82. (PMID: 10760174)
      Nat Struct Mol Biol. 2016 Jun;23(6):574-9. (PMID: 27183195)
      Proc Natl Acad Sci U S A. 2013 May 28;110(22):8864-9. (PMID: 23610425)
      Methods Enzymol. 2008;447:83-98. (PMID: 19161839)
      Annu Rev Genet. 2014;48:537-59. (PMID: 25292357)
      Nucleic Acids Res. 2015 Jul 1;43(W1):W389-94. (PMID: 25883141)
      Mol Cell. 2007 Jul 6;27(1):79-90. (PMID: 17612492)
      Biochim Biophys Acta. 2013 Jun-Jul;1829(6-7):580-9. (PMID: 23287066)
      Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):3865-9. (PMID: 8632981)
      J Bacteriol. 1988 May;170(5):2031-9. (PMID: 3283102)
      J Biol Chem. 2015 Apr 10;290(15):9478-86. (PMID: 25657006)
      J Biol Chem. 2003 Apr 4;278(14):12574-8. (PMID: 12551907)
      Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. (PMID: 20124702)
      J Biol Chem. 2015 Apr 10;290(15):9487-99. (PMID: 25657011)
      RNA. 2003 Feb;9(2):231-8. (PMID: 12554866)
      Mol Microbiol. 2004 Nov;54(4):1063-75. (PMID: 15522087)
      J Bacteriol. 2003 Nov;185(22):6530-9. (PMID: 14594825)
      Nucleic Acids Res. 2014 Nov 10;42(20):12746-57. (PMID: 25313159)
      J Mol Biol. 2006 Apr 21;358(1):8-15. (PMID: 16516921)
      Nat Rev Microbiol. 2013 Jan;11(1):45-57. (PMID: 23241849)
      Mol Cell. 2017 Jul 6;67(1):44-54.e6. (PMID: 28673541)
      J Bacteriol. 1987 Apr;169(4):1454-9. (PMID: 3031013)
      Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):10109-13. (PMID: 1946430)
      Infect Immun. 2002 Nov;70(11):6346-54. (PMID: 12379714)
      J Mol Biol. 2007 Sep 21;372(3):774-97. (PMID: 17681537)
      Biochem Soc Trans. 2014 Dec;42(6):1679-83. (PMID: 25399589)
      Methods Mol Biol. 2016;1320:11-20. (PMID: 26227034)
      Nature. 2008 Jan 17;451(7176):355-8. (PMID: 18202662)
      Acta Crystallogr D Biol Crystallogr. 2010 Sep;66(Pt 9):1036-40. (PMID: 20823555)
      Mol Microbiol. 2012 Dec;86(5):1063-72. (PMID: 22989003)
      Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2758-63. (PMID: 14981237)
      Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):125-32. (PMID: 20124692)
      Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6640-5. (PMID: 10829079)
    • Grant Information:
      R01 GM112940 United States GM NIGMS NIH HHS; T32 GM007308 United States GM NIGMS NIH HHS; R01 AI108889 United States AI NIAID NIH HHS; R01 GM035769 United States GM NIGMS NIH HHS; P30 EB009998 United States EB NIBIB NIH HHS; T32 AI007180 United States AI NIAID NIH HHS
    • الرقم المعرف:
      0 (Escherichia coli Proteins)
      0 (RNA, Messenger)
      EC 3.6.- (Acid Anhydride Hydrolases)
      EC 3.6.1.- (RppH protein, E coli)
      EC 5.1.1.- (Amino Acid Isomerases)
      EC 5.1.1.7 (DapF protein, E coli)
      EC 5.1.1.7 (diaminopimelate epimerase)
    • الموضوع:
      Date Created: 20180508 Date Completed: 20190805 Latest Revision: 20190918
    • الموضوع:
      20250114
    • الرقم المعرف:
      PMC6061855
    • الرقم المعرف:
      10.1093/nar/gky327
    • الرقم المعرف:
      29733359