5wt3: Difference between revisions
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The | ==Pyrococcus abyssi methyltransferase PaTrm5a bound by MTA and cognate tRNA== | ||
<StructureSection load='5wt3' size='340' side='right'caption='[[5wt3]], [[Resolution|resolution]] 3.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5wt3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WT3 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]] 3.204Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</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=5wt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wt3 OCA], [https://pdbe.org/5wt3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wt3 RCSB], [https://www.ebi.ac.uk/pdbsum/5wt3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wt3 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/TAW22_PYRAB TAW22_PYRAB] Catalyzes both the N1-methylation of guanosine and the C7-methylation of 4-demethylwyosine (imG-14) at position 37 in tRNA(Phe).<ref>PMID:20382657</ref> <ref>PMID:27852927</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The wyosine derivatives present at position 37 in transfer RNAs (tRNAs) are critical for reading frame maintenance. The methyltransferase Trm5a from Pyrococcus abyssi (PaTrm5a) plays a key role in this hypermodification process in generating m(1)G37 and imG2, two products of the wyosine biosynthetic pathway, through two methyl transfers to distinct substrates, but the mechanism is currently unknown. We report two cocrystal structures of PaTrm5a in complex with tRNA(Phe) and reveal the structural basis for substrate recognition, which was supported by in vitro activity assays. The crystal structures showed that the D1 domain of the enzyme undergoes large conformational changes upon the binding of tRNA. The deletion of this domain greatly reduces the affinity and activity of PaTrm5a toward its RNA substrate, indicating that the enzyme recognizes the overall shape of tRNA. Using the small-angle x-ray scattering technique and crystallographic analysis, we discovered that PaTrm5a adopts distinct open conformations before and after the binding of tRNA. Last, through structure comparison with its ortholog Methanococcus jannaschii Trm5b (MjTrm5b), we propose a reaction mechanism for the double methylation capability of this unique enzyme. | |||
Structural insight into the methyltransfer mechanism of the bifunctional Trm5.,Wang C, Jia Q, Zeng J, Chen R, Xie W Sci Adv. 2017 Dec 1;3(12):e1700195. doi: 10.1126/sciadv.1700195. eCollection 2017, Dec. PMID:29214216<ref>PMID:29214216</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 5wt3" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Pyrococcus abyssi GE5]] | |||
[[Category: Jia Q]] | |||
[[Category: Wang C]] | |||
[[Category: Xie W]] | |||
Latest revision as of 19:53, 8 November 2023
Pyrococcus abyssi methyltransferase PaTrm5a bound by MTA and cognate tRNAPyrococcus abyssi methyltransferase PaTrm5a bound by MTA and cognate tRNA
Structural highlights
FunctionTAW22_PYRAB Catalyzes both the N1-methylation of guanosine and the C7-methylation of 4-demethylwyosine (imG-14) at position 37 in tRNA(Phe).[1] [2] Publication Abstract from PubMedThe wyosine derivatives present at position 37 in transfer RNAs (tRNAs) are critical for reading frame maintenance. The methyltransferase Trm5a from Pyrococcus abyssi (PaTrm5a) plays a key role in this hypermodification process in generating m(1)G37 and imG2, two products of the wyosine biosynthetic pathway, through two methyl transfers to distinct substrates, but the mechanism is currently unknown. We report two cocrystal structures of PaTrm5a in complex with tRNA(Phe) and reveal the structural basis for substrate recognition, which was supported by in vitro activity assays. The crystal structures showed that the D1 domain of the enzyme undergoes large conformational changes upon the binding of tRNA. The deletion of this domain greatly reduces the affinity and activity of PaTrm5a toward its RNA substrate, indicating that the enzyme recognizes the overall shape of tRNA. Using the small-angle x-ray scattering technique and crystallographic analysis, we discovered that PaTrm5a adopts distinct open conformations before and after the binding of tRNA. Last, through structure comparison with its ortholog Methanococcus jannaschii Trm5b (MjTrm5b), we propose a reaction mechanism for the double methylation capability of this unique enzyme. Structural insight into the methyltransfer mechanism of the bifunctional Trm5.,Wang C, Jia Q, Zeng J, Chen R, Xie W Sci Adv. 2017 Dec 1;3(12):e1700195. doi: 10.1126/sciadv.1700195. eCollection 2017, Dec. PMID:29214216[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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