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==Crystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH bound to a non-hydrolysable triphosphorylated dinucleotide RNA (pcp-pGpG) - first guanosine residue in guanosine binding pocket==
==Crystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH bound to a non-hydrolysable triphosphorylated dinucleotide RNA (pcp-pGpG) - first guanosine residue in guanosine binding pocket==
<StructureSection load='4jzu' size='340' side='right' caption='[[4jzu]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='4jzu' size='340' side='right'caption='[[4jzu]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4jzu]] is a 3 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=4JZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JZU FirstGlance]. <br>
<table><tr><td colspan='2'>[[4jzu]] is a 3 chain structure with sequence from [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=4JZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JZU FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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]] 1.7&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GCP:PHOSPHOMETHYLPHOSPHONIC+ACID+GUANYLATE+ESTER'>GCP</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GCP:PHOSPHOMETHYLPHOSPHONIC+ACID+GUANYLATE+ESTER'>GCP</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4jzs|4jzs]], [[4jzt|4jzt]], [[4jzv|4jzv]]</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=4jzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jzu OCA], [https://pdbe.org/4jzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jzu RCSB], [https://www.ebi.ac.uk/pdbsum/4jzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jzu ProSAT]</span></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU30630, mutTA, ytkD ([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/8-oxo-dGTP_diphosphatase 8-oxo-dGTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.55 3.6.1.55] </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=4jzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jzu OCA], [http://pdbe.org/4jzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jzu RCSB], [http://www.ebi.ac.uk/pdbsum/4jzu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jzu ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/YTKD_BACSU YTKD_BACSU]
The initiation of mRNA degradation often requires deprotection of its 5' end. In eukaryotes, the 5'-methylguanosine (cap) structure is principally removed by the Nudix family decapping enzyme Dcp2, yielding a 5'-monophosphorylated RNA that is a substrate for 5' exoribonucleases. In bacteria, the 5'-triphosphate group of primary transcripts is also converted to a 5' monophosphate by a Nudix protein called RNA pyrophosphohydrolase (RppH), allowing access to both endo- and 5' exoribonucleases. Here we present the crystal structures of Bacillus subtilis RppH (BsRppH) bound to GTP and to a triphosphorylated dinucleotide RNA. In contrast to Bdellovibrio bacteriovorus RppH, which recognizes the first nucleotide of its RNA targets, the B. subtilis enzyme has a binding pocket that prefers guanosine residues in the second position of its substrates. The identification of sequence specificity for RppH in an internal position was a highly unexpected result. NMR chemical shift mapping in solution shows that at least three nucleotides are required for unambiguous binding of RNA. Biochemical assays of BsRppH on RNA substrates with single-base-mutation changes in the first four nucleotides confirm the importance of guanosine in position two for optimal enzyme activity. Our experiments highlight important structural and functional differences between BsRppH and the RNA deprotection enzymes of distantly related bacteria.
 
Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates.,Piton J, Larue V, Thillier Y, Dorleans A, Pellegrini O, Li de la Sierra-Gallay I, Vasseur JJ, Debart F, Tisne C, Condon C Proc Natl Acad Sci U S A. 2013 Apr 22. PMID:23610407<ref>PMID:23610407</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4jzu" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[7%2C8-dihydro-8-oxoguanine triphosphatase|7%2C8-dihydro-8-oxoguanine triphosphatase]]
*[[7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures|7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: 8-oxo-dGTP diphosphatase]]
[[Category: Bacillus subtilis subsp. subtilis str. 168]]
[[Category: Bacsu]]
[[Category: Large Structures]]
[[Category: Condon, C]]
[[Category: Condon C]]
[[Category: Debart, F]]
[[Category: Debart F]]
[[Category: Dorleans, A]]
[[Category: Dorleans A]]
[[Category: Larue, V]]
[[Category: Larue V]]
[[Category: Pellegrini, O]]
[[Category: Li de la Sierra-Gallay I]]
[[Category: Piton, J]]
[[Category: Pellegrini O]]
[[Category: Sierra-Gallay, I Li de la]]
[[Category: Piton J]]
[[Category: Thillier, Y]]
[[Category: Thillier Y]]
[[Category: Tisne, C]]
[[Category: Tisne C]]
[[Category: Vasseur, J J]]
[[Category: Vasseur JJ]]
[[Category: Cytosol]]
[[Category: Hydrolase]]
[[Category: Hydrolase-rna complex]]
[[Category: Nudix hydrolase]]
[[Category: Rna pyrophosphohydrolase]]
[[Category: Rpph]]

Latest revision as of 15:07, 1 March 2024

Crystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH bound to a non-hydrolysable triphosphorylated dinucleotide RNA (pcp-pGpG) - first guanosine residue in guanosine binding pocketCrystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH bound to a non-hydrolysable triphosphorylated dinucleotide RNA (pcp-pGpG) - first guanosine residue in guanosine binding pocket

Structural highlights

4jzu is a 3 chain structure with sequence from 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 1.7Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YTKD_BACSU

See Also

4jzu, resolution 1.70Å

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