Ribonuclease

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spinqualitylabelsall models Ribonuclease A (magenta) complex with thymidylic acid DNA tetramer (pink), 1rta Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Function Ribonuclease (RNase) degrades RNA. The endonucleases cleave single or double stranded RNA and include RNase III, A, T1 H and P. Exo-RNases remove terminal nucleotide from the ends of the RNA molecule. They include RNase II D, T, PH, Polynucleotide Phosphorylase (PNPase) and oligoribonuclease (ORNase). RNase A or RNase I endonuclease which cleaves C or U of single-stranded RNA (ssRNA)[1]. RNase BA is RNase from Bacillus amyloliquefaciens. RNase D exonuclease which degrades 3'-end pre-tRNA[2]. RNase H endonuclease which cleaves RNA/DNA double-strand to produce ssDNA[3]. RNase II exonuclease which degrades 3'-end ssRNA[4]. RNase III endonuclease which cleaves double stranded rRNA[5]. RNase III Dicer cleaves dsRNA to small interfering RNA and microRNA[6]. RNase 4 is the shortest RNase. It shows a high specificity for uridine[7]. RNase 5 is known as angiogenin and is a potent stimulator of new blood vessels formation[8]. RNase 6 is a cationic secreted protein with a role in host defense[9]. RNase 7 is an innate immune defense antimacrobial protein[10]. RNase E is an endonuclease which plays a role in all aspects of RNA metabolism[11]. RNase J has exonuclease activity and plays a role in RNA maturation and decay[12]. RNase L activates the inflammasome during viral infection[13]. RNase P is an endonuclease which is a ribozyme[14]. RNase S is RNase A cleaved by subtilisin. RNase SA is RNase from Streptomyces auerofaciens[15]. RNase T exonuclease which is involved in RNA maturation[16]. RNase T1 endonuclease which cleaves 3'-end G from ssRNA[17]. RNase U2 cleaves 3'-end A from ssRNA[18]. α-sarcin is a cytotoxic RNase which cleaves a phosphodiester bond in a conserved rRNA loop and inactivates the ribosome[19]. oligoribonuclease exonuclease which is an exoribonuclease which cleaves 3'-end of viral RNA-DNA hybrid[20]. Polynucleotide phosphorylase exonuclease which is a bifunctional enzyme which has exoribonuclease activity[21]. Binase is a microbial RNase which cleaves endonucleolyticly ssRNA[22]. Poly(A)-specific RNase cleaves exonucleolyticly the poly(A) tail[23]. For more details on RNase A see: RNase A Ribonuclease A Catalysis RNase A Oligomers RNase A NMR User:R. Jeremy Johnson/RNaseA RNaseA Nobel Prizes. For RNase B and RNase S see RNaseS RNaseB. Relevance The retroviral RNase H inhibitors are investigated as potential antiretroviral (HIV) agents. α-sarcin is a new anti tumor agent[24]. RNase Sa, RNase T1 and binase are studied as potential anticancer therapeutic agents[25]. RNase 6 and RNase 7 show potent antimicrobial activity[26]. RNase L plays a role in the antiviral response to West Nile virus[27]. Active Site of Ribonuclease A Ribonuclease A cleaves RNA strands by catalyzing a transphosphorylation reaction where the 2'-OH of the ribose sugar attacks the neighboring phosphate, releasing the ribose on the the other side of the phosphate. This structure shows ribonuclease A (in blue) bound to short DNA strand composed of four thymidines (in pink). Ribonuclease binds tightly to DNA, but since DNA is missing the 2'-OH, ribonuclease does not cleave it. are shown that are important for catalysis. The 3' carbon on the DNA is shown in red--it is the site where the 2'-OH is connected in RNA. The two histidines perform the proton transfers that are needed in the reaction, and the lysine stabilizes the intermediate that is formed as the 2'-OH attacks the phosphate. Ribonuclease cleaves RNA strands best next to cytidine and uridine nucleotides--the reason for this may be seen in a . Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space.[28]

3D Structures of Ribonuclease

Updated on 10-August-2016

References

1. ↑ Cho S, Beintema JJ, Zhang J. The ribonuclease A superfamily of mammals and birds: identifying new members and tracing evolutionary histories. Genomics. 2005 Feb;85(2):208-20. PMID:15676279 doi:http://dx.doi.org/10.1016/j.ygeno.2004.10.008
2. ↑ Cudny H, Zaniewski R, Deutscher MP. Escherichia coli RNase D. Catalytic properties and substrate specificity. J Biol Chem. 1981 Jun 10;256(11):5633-7. PMID:6263886
3. ↑ Moelling K, Broecker F, Kerrigan JE. RNase H: specificity, mechanisms of action, and antiviral target. Methods Mol Biol. 2014;1087:71-84. doi: 10.1007/978-1-62703-670-2_7. PMID:24158815 doi:http://dx.doi.org/10.1007/978-1-62703-670-2_7
4. ↑ Lu F, Taghbalout A. The Escherichia coli major exoribonuclease RNase II is a component of the RNA degradosome. Biosci Rep. 2014 Dec 23;34(6):e00166. doi: 10.1042/BSR20140113. PMID:25299745 doi:http://dx.doi.org/10.1042/BSR20140113
5. ↑ PMID:24124o76
6. ↑ Ji X. The mechanism of RNase III action: how dicer dices. Curr Top Microbiol Immunol. 2008;320:99-116. PMID:18268841
7. ↑ Terzyan SS, Peracaula R, de Llorens R, Tsushima Y, Yamada H, Seno M, Gomis-Ruth FX, Coll M. The three-dimensional structure of human RNase 4, unliganded and complexed with d(Up), reveals the basis for its uridine selectivity. J Mol Biol. 1999 Jan 8;285(1):205-14. PMID:9878400 doi:10.1006/jmbi.1998.2288
8. ↑ Kim KW, Park SH, Oh DH, Lee SH, Lim KS, Joo K, Chun YS, Chang SI, Min KM, Kim JC. Ribonuclease 5 coordinates signals for the regulation of intraocular pressure and inhibits neural apoptosis as a novel multi-functional anti-glaucomatous strategy. Biochim Biophys Acta. 2016 Feb;1862(2):145-54. doi: 10.1016/j.bbadis.2015.11.005., Epub 2015 Nov 12. PMID:26581172 doi:http://dx.doi.org/10.1016/j.bbadis.2015.11.005
9. ↑ Prats-Ejarque G, Arranz-Trullen J, Blanco JA, Pulido D, Nogues MV, Moussaoui M, Boix E. The first crystal structure of human RNase6 reveals a novel substrate binding and cleavage site arrangement. Biochem J. 2016 Mar 24. pii: BCJ20160245. PMID:27013146 doi:http://dx.doi.org/10.1042/BCJ20160245
10. ↑ Harder J, Schroder JM. RNase 7, a novel innate immune defense antimicrobial protein of healthy human skin. J Biol Chem. 2002 Nov 29;277(48):46779-84. Epub 2002 Sep 18. PMID:12244054 doi:http://dx.doi.org/10.1074/jbc.M207587200
11. ↑ Mackie GA. RNase E: at the interface of bacterial RNA processing and decay. Nat Rev Microbiol. 2013 Jan;11(1):45-57. doi: 10.1038/nrmicro2930. PMID:23241849 doi:http://dx.doi.org/10.1038/nrmicro2930
12. ↑ Condon C. What is the role of RNase J in mRNA turnover? RNA Biol. 2010 May-Jun;7(3):316-21. Epub 2010 May 26. PMID:20458164
13. ↑ Chakrabarti A, Banerjee S, Franchi L, Loo YM, Gale M Jr, Nunez G, Silverman RH. RNase L activates the NLRP3 inflammasome during viral infections. Cell Host Microbe. 2015 Apr 8;17(4):466-77. doi: 10.1016/j.chom.2015.02.010. Epub, 2015 Mar 26. PMID:25816776 doi:http://dx.doi.org/10.1016/j.chom.2015.02.010
14. ↑ Mann H, Ben-Asouli Y, Schein A, Moussa S, Jarrous N. Eukaryotic RNase P: role of RNA and protein subunits of a primordial catalytic ribonucleoprotein in RNA-based catalysis. Mol Cell. 2003 Oct;12(4):925-35. PMID:14580343
15. ↑ Shaw KL, Grimsley GR, Yakovlev GI, Makarov AA, Pace CN. The effect of net charge on the solubility, activity, and stability of ribonuclease Sa. Protein Sci. 2001 Jun;10(6):1206-15. PMID:11369859 doi:http://dx.doi.org/10.1110/ps.440101
16. ↑ Hsiao YY, Fang WH, Lee CC, Chen YP, Yuan HS. Structural insights into DNA repair by RNase T--an exonuclease processing 3' end of structured DNA in repair pathways. PLoS Biol. 2014 Mar 4;12(3):e1001803. doi: 10.1371/journal.pbio.1001803., eCollection 2014 Mar. PMID:24594808 doi:http://dx.doi.org/10.1371/journal.pbio.1001803
17. ↑ Loverix S, Winqvist A, Stromberg R, Steyaert J. Mechanism of RNase T1: concerted triester-like phosphoryl transfer via a catalytic three-centered hydrogen bond. Chem Biol. 2000 Aug;7(8):651-8. PMID:11048955
18. ↑ Noguchi S. Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate. Acta Crystallogr D Biol Crystallogr. 2010 Jul;66(Pt 7):843-9. Epub 2010 Jun 19. PMID:20606265 doi:10.1107/S0907444910019621
19. ↑ Sylvester ID, Roberts LM, Lord JM. Characterization of prokaryotic recombinant Aspergillus ribotoxin alpha-sarcin. Biochim Biophys Acta. 1997 Aug 21;1358(1):53-60. PMID:9296521
20. ↑ Datta AK, Niyogi K. A novel oligoribonuclease of Escherichia coli. II. Mechanism of action. J Biol Chem. 1975 Sep 25;250(18):7313-9. PMID:170260
21. ↑ Yehudai-Resheff S, Hirsh M, Schuster G. Polynucleotide phosphorylase functions as both an exonuclease and a poly(A) polymerase in spinach chloroplasts. Mol Cell Biol. 2001 Aug;21(16):5408-16. PMID:11463823 doi:http://dx.doi.org/10.1128/MCB.21.16.5408-5416.2001
22. ↑ Dudkina E, Kayumov A, Ulyanova V, Ilinskaya O. New insight into secreted ribonuclease structure: binase is a natural dimer. PLoS One. 2014 Dec 31;9(12):e115818. doi: 10.1371/journal.pone.0115818., eCollection 2014. PMID:25551440 doi:http://dx.doi.org/10.1371/journal.pone.0115818
23. ↑ Hirayama T, Matsuura T, Ushiyama S, Narusaka M, Kurihara Y, Yasuda M, Ohtani M, Seki M, Demura T, Nakashita H, Narusaka Y, Hayashi S. A poly(A)-specific ribonuclease directly regulates the poly(A) status of mitochondrial mRNA in Arabidopsis. Nat Commun. 2013;4:2247. doi: 10.1038/ncomms3247. PMID:23912222 doi:http://dx.doi.org/10.1038/ncomms3247
24. ↑ OLSON BH, GOERNER GL. ALPHA SARCIN, A NEW ANTITUMOR AGENT. I. ISOLATION, PURIFICATION, CHEMICAL COMPOSITION, AND THE IDENTITY OF A NEW AMINO ACID. Appl Microbiol. 1965 May;13:314-21. PMID:14325268
25. ↑ Makarov AA, Kolchinsky A, Ilinskaya ON. Binase and other microbial RNases as potential anticancer agents. Bioessays. 2008 Aug;30(8):781-90. doi: 10.1002/bies.20789. PMID:18623073 doi:http://dx.doi.org/10.1002/bies.20789
26. ↑ Becknell B, Eichler TE, Beceiro S, Li B, Easterling RS, Carpenter AR, James CL, McHugh KM, Hains DS, Partida-Sanchez S, Spencer JD. Ribonucleases 6 and 7 have antimicrobial function in the human and murine urinary tract. Kidney Int. 2015 Jan;87(1):151-61. doi: 10.1038/ki.2014.268. Epub 2014 Jul 30. PMID:25075772 doi:http://dx.doi.org/10.1038/ki.2014.268
27. ↑ Scherbik SV, Paranjape JM, Stockman BM, Silverman RH, Brinton MA. RNase L plays a role in the antiviral response to West Nile virus. J Virol. 2006 Mar;80(6):2987-99. PMID:16501108 doi:http://dx.doi.org/10.1128/JVI.80.6.2987-2999.2006
28. ↑ Birdsall DL, McPherson A. Crystal structure disposition of thymidylic acid tetramer in complex with ribonuclease A. J Biol Chem. 1992 Nov 5;267(31):22230-6. PMID:1429575