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[[Image:2nug.gif|left|200px]]


{{Structure
==Crystal structure of RNase III from Aquifex aeolicus complexed with ds-RNA at 1.7-Angstrom Resolution==
|PDB= 2nug |SIZE=350|CAPTION= <scene name='initialview01'>2nug</scene>, resolution 1.70&Aring;
<StructureSection load='2nug' size='340' side='right'caption='[[2nug]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
<table><tr><td colspan='2'>[[2nug]] is a 6 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=2NUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NUG FirstGlance]. <br>
|ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
|GENE= rnc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2nug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nug OCA], [https://pdbe.org/2nug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nug RCSB], [https://www.ebi.ac.uk/pdbsum/2nug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nug ProSAT]</span></td></tr>
|RELATEDENTRY=[[1rc7|1RC7]], [[2ez6|2EZ6]], [[1yz9|1YZ9]], [[1yyo|1YYO]], [[1yyw|1YYW]], [[2nue|2NUE]], [[2nuf|2NUF]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2nug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nug OCA], [http://www.ebi.ac.uk/pdbsum/2nug PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2nug RCSB]</span>
== Function ==
}}
[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/2nug_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2nug ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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.


'''Crystal structure of RNase III from Aquifex aeolicus complexed with ds-RNA at 1.7-Angstrom Resolution'''
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<ref>PMID:18047582</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2nug" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
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.
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
 
== References ==
==About this Structure==
<references/>
2NUG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NUG OCA].
__TOC__
 
</StructureSection>
==Reference==
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. 2007 Dec 7;67(1):143-154. Epub 2007 Nov 27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18047582 18047582]
[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
[[Category: Ribonuclease III]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Court DL]]
[[Category: Court, D L.]]
[[Category: Gan JH]]
[[Category: Gan, J H.]]
[[Category: Ji X]]
[[Category: Ji, X.]]
[[Category: Shaw G]]
[[Category: Shaw, G.]]
[[Category: Tropea JE]]
[[Category: Tropea, J E.]]
[[Category: Waugh DS]]
[[Category: Waugh, D S.]]
[[Category: dsrna]]
[[Category: endonucleolytic cleavage]]
[[Category: hydrolase/rna complex]]
[[Category: ribonuclease iii]]
[[Category: rna interference]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:08:36 2008''

Latest revision as of 13:21, 30 August 2023

Crystal structure of RNase III from Aquifex aeolicus complexed with ds-RNA at 1.7-Angstrom ResolutionCrystal structure of RNase III from Aquifex aeolicus complexed with ds-RNA at 1.7-Angstrom Resolution

Structural highlights

2nug is a 6 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 1.7Å
Ligands:
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.

See Also

References

  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:http://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

2nug, resolution 1.70Å

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