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==CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION== | |||
<StructureSection load='1evv' size='340' side='right'caption='[[1evv]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
| | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1evv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces Saccharomyces]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EVV FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</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=1evv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evv OCA], [https://pdbe.org/1evv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1evv RCSB], [https://www.ebi.ac.uk/pdbsum/1evv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1evv ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
We have re-determined the crystal structure of yeast tRNA(Phe) to 2. 0 A resolution using 15 year old crystals. The accuracy of the new structure, due both to higher resolution data and formerly unavailable refinement methods, consolidates the previous structural information, but also reveals novel details. In particular, the water structure around the tightly bound Mg(2+) is now clearly resolved, and hence provides more accurate information on the geometry of the magnesium-binding sites and the role of water molecules in coordinating the metal ions to the tRNA. We have assigned a total of ten magnesium ions and identified a partly conserved geometry for high-affinity Mg(2+ )binding. In the electron density map there is also clear density for a spermine molecule binding in the major groove of the TPsiC arm and also contacting a symmetry-related tRNA molecule. Interestingly, we have also found that two specific regions of the tRNA in the crystals are partially cleaved. The sites of hydrolysis are within the D and anticodon loops in the vicinity of Mg(2+). | |||
The crystal structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by Mg(2+) in 15-year old crystals.,Jovine L, Djordjevic S, Rhodes D J Mol Biol. 2000 Aug 11;301(2):401-14. PMID:10926517<ref>PMID:10926517</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1evv" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Non-Standard Residue|Non-Standard Residue]] | |||
== References == | |||
== | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Saccharomyces]] | [[Category: Saccharomyces]] | ||
[[Category: Djordjevic S]] | |||
[[Category: Djordjevic | [[Category: Jovine L]] | ||
[[Category: Jovine | [[Category: Rhodes D]] | ||
[[Category: Rhodes | |||
Latest revision as of 09:01, 9 August 2023
CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTIONCRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION
Structural highlights
Publication Abstract from PubMedWe have re-determined the crystal structure of yeast tRNA(Phe) to 2. 0 A resolution using 15 year old crystals. The accuracy of the new structure, due both to higher resolution data and formerly unavailable refinement methods, consolidates the previous structural information, but also reveals novel details. In particular, the water structure around the tightly bound Mg(2+) is now clearly resolved, and hence provides more accurate information on the geometry of the magnesium-binding sites and the role of water molecules in coordinating the metal ions to the tRNA. We have assigned a total of ten magnesium ions and identified a partly conserved geometry for high-affinity Mg(2+ )binding. In the electron density map there is also clear density for a spermine molecule binding in the major groove of the TPsiC arm and also contacting a symmetry-related tRNA molecule. Interestingly, we have also found that two specific regions of the tRNA in the crystals are partially cleaved. The sites of hydrolysis are within the D and anticodon loops in the vicinity of Mg(2+). The crystal structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by Mg(2+) in 15-year old crystals.,Jovine L, Djordjevic S, Rhodes D J Mol Biol. 2000 Aug 11;301(2):401-14. PMID:10926517[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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