6ia6: Difference between revisions
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The | ==Crystal structure of the bacterial Dehalococcoides mccartyi Elp3 with desulfo-CoA== | ||
<StructureSection load='6ia6' size='340' side='right'caption='[[6ia6]], [[Resolution|resolution]] 2.70Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6ia6]] 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=6IA6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IA6 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]] 2.7Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCA:DESULFO-COENZYME+A'>DCA</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=6ia6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ia6 OCA], [https://pdbe.org/6ia6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ia6 RCSB], [https://www.ebi.ac.uk/pdbsum/6ia6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ia6 ProSAT]</span></td></tr> | |||
</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;"> | |||
== Publication Abstract from PubMed == | |||
The Elongator complex catalyzes posttranscriptional tRNA modifications by attaching carboxy-methyl (cm(5)) moieties to uridine bases located in the wobble position. The catalytic subunit Elp3 is highly conserved and harbors two individual subdomains, a radical S-adenosyl methionine (rSAM) and a lysine acetyltransferase (KAT) domain. The details of its modification reaction cycle and particularly the substrate specificity of its KAT domain remain elusive. Here, we present the co-crystal structure of bacterial Elp3 (DmcElp3) bound to an acetyl-CoA analog and compare it to the structure of a monomeric archaeal Elp3 from Methanocaldococcus infernus (MinElp3). Furthermore, we identify crucial active site residues, confirm the importance of the extended N-terminus for substrate recognition and uncover the specific induction of acetyl-CoA hydrolysis by different tRNA species. In summary, our results establish the clinically relevant Elongator subunit as a non-canonical acetyltransferase and genuine tRNA modification enzyme. | |||
The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase.,Lin TY, Abbassi NEH, Zakrzewski K, Chramiec-Glabik A, Jemiola-Rzeminska M, Rozycki J, Glatt S Nat Commun. 2019 Feb 7;10(1):625. doi: 10.1038/s41467-019-08579-2. PMID:30733442<ref>PMID:30733442</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6ia6" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Dehalococcoides mccartyi BTF08]] | |||
[[Category: Large Structures]] | |||
[[Category: Glatt S]] | |||
[[Category: Lin TY]] | |||
Latest revision as of 14:50, 24 January 2024
Crystal structure of the bacterial Dehalococcoides mccartyi Elp3 with desulfo-CoACrystal structure of the bacterial Dehalococcoides mccartyi Elp3 with desulfo-CoA
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 PubMedThe Elongator complex catalyzes posttranscriptional tRNA modifications by attaching carboxy-methyl (cm(5)) moieties to uridine bases located in the wobble position. The catalytic subunit Elp3 is highly conserved and harbors two individual subdomains, a radical S-adenosyl methionine (rSAM) and a lysine acetyltransferase (KAT) domain. The details of its modification reaction cycle and particularly the substrate specificity of its KAT domain remain elusive. Here, we present the co-crystal structure of bacterial Elp3 (DmcElp3) bound to an acetyl-CoA analog and compare it to the structure of a monomeric archaeal Elp3 from Methanocaldococcus infernus (MinElp3). Furthermore, we identify crucial active site residues, confirm the importance of the extended N-terminus for substrate recognition and uncover the specific induction of acetyl-CoA hydrolysis by different tRNA species. In summary, our results establish the clinically relevant Elongator subunit as a non-canonical acetyltransferase and genuine tRNA modification enzyme. The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase.,Lin TY, Abbassi NEH, Zakrzewski K, Chramiec-Glabik A, Jemiola-Rzeminska M, Rozycki J, Glatt S Nat Commun. 2019 Feb 7;10(1):625. doi: 10.1038/s41467-019-08579-2. PMID:30733442[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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