5l7l: Difference between revisions
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<StructureSection load='5l7l' size='340' side='right'caption='[[5l7l]], [[Resolution|resolution]] 2.59Å' scene=''> | <StructureSection load='5l7l' size='340' side='right'caption='[[5l7l]], [[Resolution|resolution]] 2.59Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5l7l]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5l7l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dehalococcoides_mccartyi_BTF08 Dehalococcoides mccartyi BTF08]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L7L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5L7L 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]] 2.593Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5l7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l7l OCA], [https://pdbe.org/5l7l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5l7l RCSB], [https://www.ebi.ac.uk/pdbsum/5l7l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5l7l ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/ELP3_DEHMC ELP3_DEHMC] tRNA uridine(34) acetyltransferase, which mediates formation of carboxymethyluridine in the wobble base at position 34 in tRNAs (PubMed:27455459). The proposed mechanism is the following: (i) recruits S-adenosyl-L-methionine and cleaves it to generate a 5'-deoxyadenosine radical (5'-dA) in the radical S-adenosyl-L-methionine (rSAM) region, (ii) hydrolyzes acetyl-CoA in the N-acetyltransferase domain and (iii) an acetyl radical is formed by the products of the two domains and (iv) is transferred onto the C5 position of uridine(34) in the bound tRNA molecule. Does not show protein lysine acetyltransferase activity (By similarity).[UniProtKB:D5VRB9]<ref>PMID:27455459</ref> | |||
<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: Dehalococcoides mccartyi | [[Category: Dehalococcoides mccartyi BTF08]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Glatt | [[Category: Glatt S]] | ||
[[Category: Mueller | [[Category: Mueller CW]] | ||
Latest revision as of 19:10, 4 October 2023
Crystal Structure of Elp3 from Dehalococcoides mccartyi (390-407 GSGSG)Crystal Structure of Elp3 from Dehalococcoides mccartyi (390-407 GSGSG)
Structural highlights
FunctionELP3_DEHMC tRNA uridine(34) acetyltransferase, which mediates formation of carboxymethyluridine in the wobble base at position 34 in tRNAs (PubMed:27455459). The proposed mechanism is the following: (i) recruits S-adenosyl-L-methionine and cleaves it to generate a 5'-deoxyadenosine radical (5'-dA) in the radical S-adenosyl-L-methionine (rSAM) region, (ii) hydrolyzes acetyl-CoA in the N-acetyltransferase domain and (iii) an acetyl radical is formed by the products of the two domains and (iv) is transferred onto the C5 position of uridine(34) in the bound tRNA molecule. Does not show protein lysine acetyltransferase activity (By similarity).[UniProtKB:D5VRB9][1] Publication Abstract from PubMedDuring translation elongation, decoding is based on the recognition of codons by corresponding tRNA anticodon triplets. Molecular mechanisms that regulate global protein synthesis via specific base modifications in tRNA anticodons are receiving increasing attention. The conserved eukaryotic Elongator complex specifically modifies uridines located in the wobble base position of tRNAs. Mutations in Elongator subunits are associated with certain neurodegenerative diseases and cancer. Here we present the crystal structure of D. mccartyi Elp3 (DmcElp3) at 2.15-A resolution. Our results reveal an unexpected arrangement of Elp3 lysine acetyltransferase (KAT) and radical S-adenosyl methionine (SAM) domains, which share a large interface and form a composite active site and tRNA-binding pocket, with an iron-sulfur cluster located in the dimerization interface of two DmcElp3 molecules. Structure-guided mutagenesis studies of yeast Elp3 confirmed the relevance of our findings for eukaryotic Elp3s and should aid in understanding the cellular functions and pathophysiological roles of Elongator. Structural basis for tRNA modification by Elp3 from Dehalococcoides mccartyi.,Glatt S, Zabel R, Kolaj-Robin O, Onuma OF, Baudin F, Graziadei A, Taverniti V, Lin TY, Baymann F, Seraphin B, Breunig KD, Muller CW Nat Struct Mol Biol. 2016 Jul 25. doi: 10.1038/nsmb.3265. PMID:27455459[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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