3v9u: Difference between revisions
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<StructureSection load='3v9u' size='340' side='right'caption='[[3v9u]], [[Resolution|resolution]] 2.30Å' scene=''> | <StructureSection load='3v9u' size='340' side='right'caption='[[3v9u]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3v9u]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3v9u]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V9U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V9U FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.298Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3v9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v9u OCA], [https://pdbe.org/3v9u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v9u RCSB], [https://www.ebi.ac.uk/pdbsum/3v9u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v9u ProSAT]</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=3v9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v9u OCA], [https://pdbe.org/3v9u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v9u RCSB], [https://www.ebi.ac.uk/pdbsum/3v9u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v9u ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/RNT_ECOLI RNT_ECOLI] Responsible for the end-turnover of tRNA: specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A). Also appears to be involved in tRNA biosynthesis, especially in strains lacking other exoribonucleases.[HAMAP-Rule:MF_00157] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia coli K-12]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Hsiao | [[Category: Hsiao Y-Y]] | ||
[[Category: Yuan | [[Category: Yuan HS]] | ||
Latest revision as of 15:17, 8 November 2023
Crystal structure of RNase T in complex with a preferred ssDNA (AAT) with two Mg in the active siteCrystal structure of RNase T in complex with a preferred ssDNA (AAT) with two Mg in the active site
Structural highlights
FunctionRNT_ECOLI Responsible for the end-turnover of tRNA: specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A). Also appears to be involved in tRNA biosynthesis, especially in strains lacking other exoribonucleases.[HAMAP-Rule:MF_00157] Publication Abstract from PubMedExonucleases are key enzymes in the maintenance of genome stability, processing of immature RNA precursors and degradation of unnecessary nucleic acids. However, it remains unclear how exonucleases digest nucleic acids to generate correct end products for next-step processing. Here we show how the exonuclease RNase T stops its trimming precisely. The crystal structures of RNase T in complex with a stem-loop DNA, a GG dinucleotide and single-stranded DNA with different 3'-end sequences demonstrate why a duplex with a short 3'-overhang, a dinucleotide and a ssDNA with a 3'-end C cannot be further digested by RNase T. Several hydrophobic residues in RNase T change their conformation upon substrate binding and induce an active or inactive conformation in the active site that construct a precise machine to determine which substrate should be digested based on its sequence, length and structure. These studies thus provide mechanistic insights into how RNase T prevents over digestion of its various substrates, and the results can be extrapolated to the thousands of members of the DEDDh family of exonucleases. How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes.,Hsiao YY, Duh Y, Chen YP, Wang YT, Yuan HS Nucleic Acids Res. 2012 Jun 19. PMID:22718982[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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