5t16

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of yeast RNase III (Rnt1p) complexed with a non-hydrolyzable RNA substrate analog

Structural highlights

5t16 is a 16 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.783Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNT1_YEAST DsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed spacer (ETS) and in the 3'-ETS. In vitro, cleaves synthetic 5'-ETS RNA A0 site in the absence of snoRNA or other factors. Has an essential growth function in addition to pre-rRNA processing.

Publication Abstract from PubMed

Double-stranded RNA (dsRNA)-specific RNase III proteins are required for RNA maturation and gene regulation. The mechanism of prokaryotic RNase IIIs has been well characterized, but how eukaryotic RNase IIIs (exemplified by Rnt1p, Drosha, and Dicer) work is less clear. Recently, we reported the crystal structure of Rnt1p in complex with RNA, revealing a double-ruler mechanism for substrate selection. Here, we present more structures of Rnt1p, either RNA free or RNA bound, featuring two major conformations of the enzyme. Using these structures with existing data, we describe the functional cycle of Rnt1p in five steps, selecting, loading, locking, cleavage, and releasing. We also describe atomic details of the two-Mg2+-ion catalytic mechanism that is applicable to all eukaryotic RNase III enzymes. Overall, our results indicate that substrate selection is achieved independent of cleavage, allowing the recognition of substrates with different structures while preserving the basic mechanism of cleavage.

The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III.,Song H, Fang X, Jin L, Shaw GX, Wang YX, Ji X Structure. 2017 Feb 7;25(2):353-363. doi: 10.1016/j.str.2016.12.013. Epub 2017, Jan 19. PMID:28111020^[1]

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

References

↑ Song H, Fang X, Jin L, Shaw GX, Wang YX, Ji X. The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III. Structure. 2017 Feb 7;25(2):353-363. doi: 10.1016/j.str.2016.12.013. Epub 2017, Jan 19. PMID:28111020 doi:http://dx.doi.org/10.1016/j.str.2016.12.013

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5t16"

Categories: Large Structures | Saccharomyces cerevisiae S288C | Ji X | Song H

@@ Line 1: / Line 1: @@
 ==Crystal structure of yeast RNase III (Rnt1p) complexed with a non-hydrolyzable RNA substrate analog==
-<StructureSection load='5t16' size='340' side='right' caption='[[5t16]], [[Resolution|resolution]] 2.78&Aring;' scene=''>
+<StructureSection load='5t16' size='340' side='right'caption='[[5t16]], [[Resolution|resolution]] 2.78&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5t16]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T16 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5t16]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T16 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T16 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 2.783&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=73W:5-O-[(DITHIOPHOSPHONO)]CYTIDINE'>73W</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=73W:5-O-[(DITHIOPHOSPHONO)]CYTIDINE'>73W</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5t16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t16 OCA], [https://pdbe.org/5t16 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t16 RCSB], [https://www.ebi.ac.uk/pdbsum/5t16 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t16 ProSAT]</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=5t16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t16 OCA], [http://pdbe.org/5t16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t16 RCSB], [http://www.ebi.ac.uk/pdbsum/5t16 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t16 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RNT1_YEAST RNT1_YEAST]] DsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed spacer (ETS) and in the 3'-ETS. In vitro, cleaves synthetic 5'-ETS RNA A0 site in the absence of snoRNA or other factors. Has an essential growth function in addition to pre-rRNA processing.
+[https://www.uniprot.org/uniprot/RNT1_YEAST RNT1_YEAST] DsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed spacer (ETS) and in the 3'-ETS. In vitro, cleaves synthetic 5'-ETS RNA A0 site in the absence of snoRNA or other factors. Has an essential growth function in addition to pre-rRNA processing.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 19: @@
 </div>
 <div class="pdbe-citations 5t16" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ribonuclease III]]
+[[Category: Large Structures]]
-[[Category: Ji, X]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Song, H]]
+[[Category: Ji X]]
-[[Category: Hydrolase-rna complex]]
+[[Category: Song H]]
-[[Category: Rnase iii]]
-[[Category: Rnt1p]]
-[[Category: Substrate-loaded complex]]

5t16

From Proteopedia

Current revision

Crystal structure of yeast RNase III (Rnt1p) complexed with a non-hydrolyzable RNA substrate analog

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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