2nue: Difference between revisions

Latest revision as of 10:21, 30 August 2023

Crystal structure of RNase III from Aquifex aeolicus complexed with ds-RNA at 2.9-Angstrom Resolution

Structural highlights

2nue is a 3 chain structure with sequence from Aquifex aeolicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNC_AQUAE Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Also processes some mRNAs, and tRNAs when they are encoded in the rRNA operon.^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

RNA interference is mediated by small interfering RNAs produced by members of the ribonuclease III (RNase III) family represented by bacterial RNase III and eukaryotic Rnt1p, Drosha and Dicer. For mechanistic studies, bacterial RNase III has been a valuable model system for the family. Previously, we have shown that RNase III uses two catalytic sites to create the 2-nucleotide (nt) 3' overhangs in its products. Here, we present three crystal structures of RNase III in complex with double-stranded RNA, demonstrating how Mg(2+) is essential for the formation of a catalytically competent protein-RNA complex, how the use of two Mg(2+) ions can drive the hydrolysis of each phosphodiester bond, and how conformational changes in both the substrate and the protein are critical elements for assembling the catalytic complex. Moreover, we have modelled a protein-substrate complex and a protein-reaction intermediate (transition state) complex on the basis of the crystal structures. Together, the crystal structures and the models suggest a stepwise mechanism for RNase III to execute the phosphoryl transfer reaction.

A stepwise model for double-stranded RNA processing by ribonuclease III.,Gan J, Shaw G, Tropea JE, Waugh DS, Court DL, Ji X Mol Microbiol. 2008 Jan;67(1):143-54. Epub 2007 Nov 27. PMID:18047582^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Shi Z, Nicholson RH, Jaggi R, Nicholson AW. Characterization of Aquifex aeolicus ribonuclease III and the reactivity epitopes of its pre-ribosomal RNA substrates. Nucleic Acids Res. 2011 Apr;39(7):2756-68. doi: 10.1093/nar/gkq1030. Epub 2010, Dec 7. PMID:21138964 doi:https://dx.doi.org/10.1093/nar/gkq1030
↑ Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X. Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III. Cell. 2006 Jan 27;124(2):355-66. PMID:16439209 doi:10.1016/j.cell.2005.11.034
↑ Gan J, Shaw G, Tropea JE, Waugh DS, Court DL, Ji X. A stepwise model for double-stranded RNA processing by ribonuclease III. Mol Microbiol. 2008 Jan;67(1):143-54. Epub 2007 Nov 27. PMID:18047582 doi:10.1111/j.1365-2958.2007.06032.x

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Shi Z, Nicholson RH, Jaggi R, Nicholson AW. Characterization of Aquifex aeolicus ribonuclease III and the reactivity epitopes of its pre-ribosomal RNA substrates. Nucleic Acids Res. 2011 Apr;39(7):2756-68. doi: 10.1093/nar/gkq1030. Epub 2010, Dec 7. PMID:21138964 doi:https://dx.doi.org/10.1093/nar/gkq1030

[2] Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X. Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III. Cell. 2006 Jan 27;124(2):355-66. PMID:16439209 doi:10.1016/j.cell.2005.11.034

[3] Gan J, Shaw G, Tropea JE, Waugh DS, Court DL, Ji X. A stepwise model for double-stranded RNA processing by ribonuclease III. Mol Microbiol. 2008 Jan;67(1):143-54. Epub 2007 Nov 27. PMID:18047582 doi:10.1111/j.1365-2958.2007.06032.x

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Crystal structure of RNase III from Aquifex aeolicus complexed with ds-RNA at 2.9-Angstrom Resolution==
-<StructureSection load='2nue' size='340' side='right' caption='[[2nue]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='2nue' size='340' side='right'caption='[[2nue]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2nue]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NUE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NUE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2nue]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NUE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NUE FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1rc7|1rc7]], [[2ez6|2ez6]], [[1yz9|1yz9]], [[1yyo|1yyo]], [[1yyw|1yyw]], [[2nuf|2nuf]], [[2nug|2nug]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rnc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2nue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nue OCA], [https://pdbe.org/2nue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nue RCSB], [https://www.ebi.ac.uk/pdbsum/2nue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nue ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2nue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nue OCA], [http://pdbe.org/2nue PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2nue RCSB], [http://www.ebi.ac.uk/pdbsum/2nue PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2nue ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RNC_AQUAE RNC_AQUAE]] Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Also processes some mRNAs, and tRNAs when they are encoded in the rRNA operon.<ref>PMID:21138964</ref> <ref>PMID:16439209</ref>
+[https://www.uniprot.org/uniprot/RNC_AQUAE RNC_AQUAE] Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Also processes some mRNAs, and tRNAs when they are encoded in the rRNA operon.<ref>PMID:21138964</ref> <ref>PMID:16439209</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nu/2nue_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nu/2nue_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 32: / Line 30: @@
 ==See Also==
-*[[Ribonuclease|Ribonuclease]]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-*[[Temp|Temp]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Aquifex aeolicus huber and stetter 2001]]
+[[Category: Aquifex aeolicus]]
-[[Category: Ribonuclease III]]
+[[Category: Large Structures]]
-[[Category: Court, D L]]
+[[Category: Court DL]]
-[[Category: Gan, J H]]
+[[Category: Gan JH]]
-[[Category: Ji, X]]
+[[Category: Ji X]]
-[[Category: Shaw, G]]
+[[Category: Shaw G]]
-[[Category: Tropea, J E]]
+[[Category: Tropea JE]]
-[[Category: Waugh, D S]]
+[[Category: Waugh DS]]
-[[Category: Dsrna]]
-[[Category: Endonucleolytic cleavage]]
-[[Category: Hydrolase-rna complex]]
-[[Category: Ribonuclease iii]]
-[[Category: Rna interference]]

2nue: Difference between revisions

Latest revision as of 10:21, 30 August 2023

Crystal structure of RNase III from Aquifex aeolicus complexed with ds-RNA at 2.9-Angstrom Resolution

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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