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2ez6

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Crystal structure of Aquifex aeolicus RNase III (D44N) complexed with product of double-stranded RNA processing

Structural highlights

2ez6 is a 4 chain structure with sequence from Aquifex aeolicus. The September 2008 RCSB PDB Molecule of the Month feature on Ribonuclease A by David Goodsell is 10.2210/rcsb_pdb/mom_2008_9. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.05Å
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

Members of the ribonuclease III (RNase III) family are double-stranded RNA (dsRNA) specific endoribonucleases characterized by a signature motif in their active centers and a two-base 3' overhang in their products. While Dicer, which produces small interfering RNAs, is currently the focus of intense interest, the structurally simpler bacterial RNase III serves as a paradigm for the entire family. Here, we present the crystal structure of an RNase III-product complex, the first catalytic complex observed for the family. A 7 residue linker within the protein facilitates induced fit in protein-RNA recognition. A pattern of protein-RNA interactions, defined by four RNA binding motifs in RNase III and three protein-interacting boxes in dsRNA, is responsible for substrate specificity, while conserved amino acid residues and divalent cations are responsible for scissile-bond cleavage. The structure reveals a wealth of information about the mechanism of RNA hydrolysis that can be extrapolated to other RNase III family members.

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ez6"

@@ Line 3: / Line 3: @@
 <StructureSection load='2ez6' size='340' side='right'caption='[[2ez6]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ez6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. The September 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Ribonuclease A''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_9 10.2210/rcsb_pdb/mom_2008_9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EZ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EZ6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ez6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. The September 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Ribonuclease A''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_9 10.2210/rcsb_pdb/mom_2008_9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EZ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EZ6 FirstGlance]. <br>
-</td></tr><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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1jfz|1jfz]], [[1o0w|1o0w]], [[1rc7|1rc7]], [[1yz9|1yz9]], [[1yyo|1yyo]], [[1yyw|1yyw]], [[1rc5|1rc5]], [[1yyk|1yyk]]</div></td></tr>
+<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>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rnc ([https://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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=2ez6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ez6 OCA], [https://pdbe.org/2ez6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ez6 RCSB], [https://www.ebi.ac.uk/pdbsum/2ez6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ez6 ProSAT]</span></td></tr>
 </table>
 == 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>
+[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]]
@@ Line 38: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Aquifex aeolicus huber and stetter 2001]]
+[[Category: Aquifex aeolicus]]
 [[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
 [[Category: Ribonuclease A]]
-[[Category: Ribonuclease III]]
+[[Category: Austin BP]]
-[[Category: Austin, B P]]
+[[Category: Court DL]]
-[[Category: Court, D L]]
+[[Category: Gan J]]
-[[Category: Gan, J]]
+[[Category: Ji X]]
-[[Category: Ji, X]]
+[[Category: Tropea JE]]
-[[Category: Tropea, J E]]
+[[Category: Waugh DS]]
-[[Category: Waugh, D S]]
-[[Category: Dsrna]]
-[[Category: Hydrolase-rna complex]]
-[[Category: Ribonuclease iii]]
-[[Category: Rna interference]]
-[[Category: Rna processing]]

2ez6

From Proteopedia

Current revision

Crystal structure of Aquifex aeolicus RNase III (D44N) complexed with product of double-stranded RNA processing

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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