Ribonuclease

From Proteopedia

(Difference between revisions)

Revision as of 09:49, 10 August 2016

Ribonuclease A (magenta) complex with thymidylic acid DNA tetramer (pink), 1rta

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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 MC1 from bitter gourd has a preference for cleavage at the 5'-end of uridine^[14].
RNase P is an endonuclease which is a ribozyme^[15].
RNase PH is an exonuclease involved in the trimming of the 3' terminus of tRNA^[16].
RNase Po1 is a G-specific RNase from Pleurotus ostreatus.
RNase RH is RNase from Rhizopus niveus^[17].
RNase S is RNase A cleaved by subtilisin.
RNase SA is RNase from Streptomyces auerofaciens^[18].
RNase T exonuclease which is involved in RNA maturation^[19].
RNase T1 endonuclease which cleaves 3'-end G from ssRNA^[20].
RNase U2 cleaves 3'-end A from ssRNA^[21].
α-sarcin is a cytotoxic RNase which cleaves a phosphodiester bond in a conserved rRNA loop and inactivates the ribosome^[22].
oligoribonuclease exonuclease which is an exoribonuclease which cleaves 3'-end of viral RNA-DNA hybrid^[23].
Polynucleotide phosphorylase exonuclease which is a bifunctional enzyme which has exoribonuclease activity^[24].
Binase is a microbial RNase which cleaves endonucleolyticly ssRNA^[25].
Poly(A)-specific RNase cleaves exonucleolyticly the poly(A) tail^[26].

For more details on RNase A see:

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^[27]. RNase Sa, RNase T1 and binase are studied as potential anticancer therapeutic agents^[28]. RNase 6 and RNase 7 show potent antimicrobial activity^[29]. RNase L plays a role in the antiviral response to West Nile virus^[30]. Human tumor cells proliferation is inhibited by tRNase Po1^[31].

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.^[32]

3D Structures of Ribonuclease

Updated on 10-August-2016

References

↑ 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
↑ 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
↑ 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
↑ 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
↑ PMID:24124o76
↑ Ji X. The mechanism of RNase III action: how dicer dices. Curr Top Microbiol Immunol. 2008;320:99-116. PMID:18268841
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ Suzuki A, Yao M, Tanaka I, Numata T, Kikukawa S, Yamasaki N, Kimura M. Crystal structures of the ribonuclease MC1 from bitter gourd seeds, complexed with 2'-UMP or 3'-UMP, reveal structural basis for uridine specificity. Biochem Biophys Res Commun. 2000 Aug 28;275(2):572-6. PMID:10964705 doi:10.1006/bbrc.2000.3318
↑ 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
↑ Deutscher MP, Marshall GT, Cudny H. RNase PH: an Escherichia coli phosphate-dependent nuclease distinct from polynucleotide phosphorylase. Proc Natl Acad Sci U S A. 1988 Jul;85(13):4710-4. PMID:2455297
↑ Kurihara H, Mitsui Y, Ohgi K, Irie M, Mizuno H, Nakamura KT. Crystal and molecular structure of RNase Rh, a new class of microbial ribonuclease from Rhizopus niveus. FEBS Lett. 1992 Jul 20;306(2-3):189-92. PMID:1633875
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ Kobayashi H, Motoyoshi N, Itagaki T, Tabata K, Suzuki T, Inokuchi N. The inhibition of human tumor cell proliferation by RNase Pol, a member of the RNase T1 family, from Pleurotus ostreatus. Biosci Biotechnol Biochem. 2013;77(7):1486-91. Epub 2013 Jul 7. PMID:23832341 doi:http://dx.doi.org/10.1271/bbb.130133
↑ 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

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Wayne Decatur, David Canner, Joel L. Sussman, Jaime Prilusky

Retrieved from "http://52.214.119.220/wiki/index.php/Ribonuclease"

@@ Line 16: / Line 16: @@
 *  '''RNase J''' has exonuclease activity and plays a role in RNA maturation and decay<ref>PMID:20458164</ref>.<br />
 *  '''RNase L''' activates the inflammasome during viral infection<ref>PMID:25816776</ref>.<br />
+*  '''RNase MC1''' from bitter gourd has a preference for cleavage at the 5'-end of uridine<ref>PMID:10964705</ref>.<br />
 *  '''RNase P''' is an endonuclease which is a ribozyme<ref>PMID:14580343</ref>.<br />
+*  '''RNase PH''' is an exonuclease involved in the trimming of the 3' terminus of tRNA<ref>PMID:2455297</ref>.<br />
+*  '''RNase Po1''' is a G-specific RNase from ''Pleurotus ostreatus''.<br />
+*  '''RNase RH''' is RNase from ''Rhizopus niveus''<ref>PMID:1633875</ref>.<br />
 *  '''RNase S''' is RNase A cleaved by subtilisin.<br />
 *  '''RNase SA''' is RNase from ''Streptomyces auerofaciens''<ref>PMID:11369859</ref>.<br />
@@ Line 38: / Line 42: @@
 == Relevance ==
-The retroviral RNase H inhibitors are investigated as potential antiretroviral (HIV) agents.  α-sarcin is a new anti tumor agent<ref>PMID:14325268</ref>.  RNase Sa, RNase T1 and binase are studied as potential anticancer therapeutic agents<ref>PMID:18623073</ref>.  RNase 6 and RNase 7 show potent antimicrobial activity<ref>PMID:25075772</ref>.  RNase L plays a role in the antiviral response to West Nile virus<ref>PMID:16501108</ref>.
+The retroviral RNase H inhibitors are investigated as potential antiretroviral (HIV) agents.  α-sarcin is a new anti tumor agent<ref>PMID:14325268</ref>.  RNase Sa, RNase T1 and binase are studied as potential anticancer therapeutic agents<ref>PMID:18623073</ref>.  RNase 6 and RNase 7 show potent antimicrobial activity<ref>PMID:25075772</ref>.  RNase L plays a role in the antiviral response to West Nile virus<ref>PMID:16501108</ref>.  Human tumor cells proliferation is inhibited by tRNase Po1<ref>PMID:23832341</ref>.
 ==Active Site of Ribonuclease A==

Ribonuclease

From Proteopedia

Revision as of 09:49, 10 August 2016

Function

Relevance

Active Site of Ribonuclease A

3D Structures of Ribonuclease

References

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