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==Crystal structure of phenylalanine tRNA from Escherichia coli==
==Crystal structure of phenylalanine tRNA from Escherichia coli==
<StructureSection load='6y3g' size='340' side='right'caption='[[6y3g]]' scene=''>
<StructureSection load='6y3g' size='340' side='right'caption='[[6y3g]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y3G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y3G FirstGlance]. <br>
<table><tr><td colspan='2'>[[6y3g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y3G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y3G FirstGlance]. <br>
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6y3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y3g OCA], [http://pdbe.org/6y3g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y3g RCSB], [http://www.ebi.ac.uk/pdbsum/6y3g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y3g ProSAT]</span></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]] 3.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3AU:3-[(3S)-3-AMINO-3-CARBOXYPROPYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>3AU</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></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=6y3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y3g OCA], [https://pdbe.org/6y3g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y3g RCSB], [https://www.ebi.ac.uk/pdbsum/6y3g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y3g ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cyclodipeptide synthases (CDPSs) catalyze the synthesis of various cyclodipeptides by using two aminoacyl-tRNA (aa-tRNA) substrates in a sequential mechanism. Here, we studied binding of phenylalanyl-tRNA(Phe) to the CDPS from Candidatus Glomeribacter gigasporarum (Cglo-CDPS) by gel filtration and electrophoretic mobility shift assay. We determined the crystal structure of the Cglo-CDPS:Phe-tRNA(Phe) complex to 5 A resolution and further studied it in solution using small-angle X-ray scattering (SAXS). The data show that the major groove of the acceptor stem of the aa-tRNA interacts with the enzyme through the basic beta2 and beta7 strands of CDPSs belonging to the XYP subfamily. A bending of the CCA extremity enables the amino acid moiety to be positioned in the P1 pocket while the terminal A76 adenosine occupies the P2 pocket. Such a positioning indicates that the present structure illustrates the binding of the first aa-tRNA. In cells, CDPSs and the elongation factor EF-Tu share aminoacylated tRNAs as substrates. The present study shows that CDPSs and EF-Tu interact with opposite sides of tRNA. This may explain how CDPSs hijack aa-tRNAs from canonical ribosomal protein synthesis.
Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates.,Bourgeois G, Seguin J, Babin M, Gondry M, Mechulam Y, Schmitt E RNA. 2020 Nov;26(11):1589-1602. doi: 10.1261/rna.075184.120. Epub 2020 Jul 17. PMID:32680846<ref>PMID:32680846</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6y3g" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bourgeois G]]
[[Category: Bourgeois G]]
[[Category: Mechulam Y]]
[[Category: Mechulam Y]]
[[Category: Schmitt E]]
[[Category: Schmitt E]]

Latest revision as of 13:18, 24 January 2024

Crystal structure of phenylalanine tRNA from Escherichia coli

6y3g, resolution 3.10Å

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