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Ribonuclease
From Proteopedia
(Difference between revisions)
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* '''RNase H''' endonuclease which cleaves RNA/DNA double-strand to produce ssDNA<ref>PMID:24158815</ref>.<br /> | * '''RNase H''' endonuclease which cleaves RNA/DNA double-strand to produce ssDNA<ref>PMID:24158815</ref>.<br /> | ||
* '''RNase II''' exonuclease which degrades 3'-end ssRNA<ref>PMID:25299745</ref>.<br /> | * '''RNase II''' exonuclease which degrades 3'-end ssRNA<ref>PMID:25299745</ref>.<br /> | ||
| - | * '''RNase III''' endonuclease which cleaves rRNA.<br /> | + | * '''RNase III''' endonuclease which cleaves double stranded rRNA<ref>PMID:24124o76</ref>.<br /> |
| - | * '''RNase III Dicer''' cleaves dsRNA to small interfering RNA and microRNA.<br /> | + | * '''RNase III Dicer''' cleaves dsRNA to small interfering RNA and microRNA<ref>PMID:18268841</ref>.<br /> |
| - | * '''RNase 5''' is known as angiogenin and is a potent stimulator of new blood vessels formation.<br /> | + | * '''RNase 5''' is known as angiogenin and is a potent stimulator of new blood vessels formation<ref>PMID:26581172</ref>.<br /> |
| - | * '''RNase P''' endonuclease which is a ribozyme.<br /> | + | * '''RNase P''' endonuclease which is a ribozyme<ref>PMID:14580343</ref>.<br /> |
* '''RNase S''' is RNase A cleaved by subtilisin.<br /> | * '''RNase S''' is RNase A cleaved by subtilisin.<br /> | ||
| - | * '''RNase SA''' is RNase from ''Streptomyces auerofaciens''.<br /> | + | * '''RNase SA''' is RNase from ''Streptomyces auerofaciens''<ref>PMID:11369859</ref>.<br /> |
| - | * '''RNase T''' exonuclease which is involved in RNA maturation.<br /> | + | * '''RNase T''' exonuclease which is involved in RNA maturation<ref>PMID:24594808</ref>.<br /> |
| - | * '''RNase T1''' endonuclease which cleaves 3'-end G from ssRNA.<br /> | + | * '''RNase T1''' endonuclease which cleaves 3'-end G from ssRNA<ref>PMID:11048955</ref>.<br /> |
| - | * '''RNase U2''' cleaves 3'-end A from ssRNA.<br /> | + | * '''RNase U2''' cleaves 3'-end A from ssRNA<ref>PMID:20606265</ref>.<br /> |
| - | * '''α-sarcin''' is a cytotoxic RNase which cleaves a phosphodiester bond in a conserved rRNA loop and inactivates the ribosome.<br /> | + | * '''α-sarcin''' is a cytotoxic RNase which cleaves a phosphodiester bond in a conserved rRNA loop and inactivates the ribosome<ref>PMID:9296521</ref>.<br /> |
* '''oligoribonuclease''' exonuclease which is an exoribonuclease which cleaves 3'-end of viral RNA-DNA hybrid.<br /> | * '''oligoribonuclease''' exonuclease which is an exoribonuclease which cleaves 3'-end of viral RNA-DNA hybrid.<br /> | ||
* '''Polynucleotide phosphorylase''' exonuclease which is a bifunctional enzyme which has exoribonuclease activity.<br /> | * '''Polynucleotide phosphorylase''' exonuclease which is a bifunctional enzyme which has exoribonuclease activity.<br /> | ||
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== Relevance == | == Relevance == | ||
| - | The retroviral RNase H inhibitors are investigated as potential antiretroviral (HIV) agents. | + | The retroviral RNase H inhibitors are investigated as potential antiretroviral (HIV) agents. α-sarcin is a new anti tumor agent<ref>PMID:14325268</ref>. |
| - | {{Clear}} | ||
==Active Site of Ribonuclease A== | ==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. <scene name='Goodsell_Sandbox/Ribonuclease_catalytic_site/2'>Three amino acids</scene> 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 <scene name='Goodsell_Sandbox/Ribonuclease_recognition/2'>spacefilling representation</scene>. Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space.<ref>PMID:1429575</ref> | 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. <scene name='Goodsell_Sandbox/Ribonuclease_catalytic_site/2'>Three amino acids</scene> 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 <scene name='Goodsell_Sandbox/Ribonuclease_recognition/2'>spacefilling representation</scene>. Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space.<ref>PMID:1429575</ref> | ||
Revision as of 08:41, 10 August 2016
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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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
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