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==Crystal structure of RNase Z in complex with precursor tRNA(Thr)==
==Crystal structure of RNase Z in complex with precursor tRNA(Thr)==
<StructureSection load='4gcw' size='340' side='right' caption='[[4gcw]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
<StructureSection load='4gcw' size='340' side='right'caption='[[4gcw]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4gcw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GCW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GCW FirstGlance]. <br>
<table><tr><td colspan='2'>[[4gcw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GCW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GCW FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1y44|1y44]], [[2fk6|2fk6]]</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=4gcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gcw OCA], [https://pdbe.org/4gcw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gcw RCSB], [https://www.ebi.ac.uk/pdbsum/4gcw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gcw ProSAT]</span></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU23840, rnz, yqjK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_Z Ribonuclease Z], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.11 3.1.26.11] </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=4gcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gcw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gcw RCSB], [http://www.ebi.ac.uk/pdbsum/4gcw PDBsum]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/RNZ_BACSU RNZ_BACSU] Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA.<ref>PMID:12941704</ref>  
Ribonuclease (RNase) Z is involved in the maturation of the 3' ends of transfer RNAs (tRNAs) in all three kingdoms of life. To prevent futile cycles of CCA addition and removal, eukaryotic RNase Z discriminates against mature tRNAs bearing a CCA motif, with the first cytosine residue (C74) being the key antideterminant. Here, we show that, remarkably, the B. subtilis enzyme does not discriminate against cytosine in position 74, but rather is highly stimulated by uracil in this location. Consistent with this observation, the vast majority of B. subtilis tRNA precursor substrates of RNase Z naturally contain U74. Those tRNA precursors with a uracil further downstream are also substrates for RNase Z, but are matured in a two-step endo/exonuclease reaction. We solved the first crystal structure of B. subtilis RNase Z bound to a tRNA(Thr) precursor with U74 and show that the enzyme has a specific binding pocket for this nucleotide.
 
Activation of tRNA maturation by downstream uracil residues in B. subtilis.,Pellegrini O, Li de la Sierra-Gallay I, Piton J, Gilet L, Condon C Structure. 2012 Oct 10;20(10):1769-77. doi: 10.1016/j.str.2012.08.002. Epub 2012 , Aug 30. PMID:22940585<ref>PMID:22940585</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Ribonuclease|Ribonuclease]]
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
*[[User:Jaime.Prilusky/Test/tree|User:Jaime.Prilusky/Test/tree]]
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacsu]]
[[Category: Bacillus subtilis]]
[[Category: Ribonuclease Z]]
[[Category: Bacillus subtilis subsp. subtilis str. 168]]
[[Category: Condon, C]]
[[Category: Large Structures]]
[[Category: Gilet, L]]
[[Category: Condon C]]
[[Category: Pellegrini, O]]
[[Category: Gilet L]]
[[Category: Piton, J]]
[[Category: Li de la Sierra-Gallay I]]
[[Category: Sierra-Gallay, I Li de la]]
[[Category: Pellegrini O]]
[[Category: Hydrolase-rna complex]]
[[Category: Piton J]]
[[Category: Protein-rna complex]]
[[Category: Trna binding]]
[[Category: Trna maturase]]
[[Category: Zinc-dependent metalo betalactamase - rna complex]]

Latest revision as of 18:43, 14 March 2024

Crystal structure of RNase Z in complex with precursor tRNA(Thr)Crystal structure of RNase Z in complex with precursor tRNA(Thr)

Structural highlights

4gcw is a 2 chain structure with sequence from Bacillus subtilis and Bacillus subtilis subsp. subtilis str. 168. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNZ_BACSU Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA.[1]

See Also

References

  1. ↑ Pellegrini O, Nezzar J, Marchfelder A, Putzer H, Condon C. Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis. EMBO J. 2003 Sep 1;22(17):4534-43. PMID:12941704 doi:http://dx.doi.org/10.1093/emboj/cdg435

4gcw, resolution 3.00Å

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