5wt3: Difference between revisions

Latest revision as of 16:53, 8 November 2023

Pyrococcus abyssi methyltransferase PaTrm5a bound by MTA and cognate tRNA

Structural highlights

5wt3 is a 2 chain structure with sequence from Pyrococcus abyssi GE5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.204Å
Ligands:	MTA
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TAW22_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 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^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ de Crecy-Lagard V, Brochier-Armanet C, Urbonavicius J, Fernandez B, Phillips G, Lyons B, Noma A, Alvarez S, Droogmans L, Armengaud J, Grosjean H. Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea. Mol Biol Evol. 2010 Sep;27(9):2062-77. doi: 10.1093/molbev/msq096. Epub 2010 Apr , 9. PMID:20382657 doi:https://dx.doi.org/10.1093/molbev/msq096
↑ Urbonavičius J, Rutkienė R, Lopato A, Tauraitė D, Stankevičiūtė J, Aučynaitė A, Kaliniene L, van Tilbeurgh H, Meškys R. Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea. RNA. 2016 Dec;22(12):1871-1883. PMID:27852927 doi:10.1261/rna.057059.116
↑ Wang C, Jia Q, Zeng J, Chen R, Xie W. Structural insight into the methyltransfer mechanism of the bifunctional Trm5. Sci Adv. 2017 Dec 1;3(12):e1700195. doi: 10.1126/sciadv.1700195. eCollection 2017, Dec. PMID:29214216 doi:https://dx.doi.org/10.1126/sciadv.1700195

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Crecy-Lagard V, Brochier-Armanet C, Urbonavicius J, Fernandez B, Phillips G, Lyons B, Noma A, Alvarez S, Droogmans L, Armengaud J, Grosjean H. Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea. Mol Biol Evol. 2010 Sep;27(9):2062-77. doi: 10.1093/molbev/msq096. Epub 2010 Apr , 9. PMID:20382657 doi:https://dx.doi.org/10.1093/molbev/msq096

[2] Urbonavičius J, Rutkienė R, Lopato A, Tauraitė D, Stankevičiūtė J, Aučynaitė A, Kaliniene L, van Tilbeurgh H, Meškys R. Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea. RNA. 2016 Dec;22(12):1871-1883. PMID:27852927 doi:10.1261/rna.057059.116

[3] Wang C, Jia Q, Zeng J, Chen R, Xie W. Structural insight into the methyltransfer mechanism of the bifunctional Trm5. Sci Adv. 2017 Dec 1;3(12):e1700195. doi: 10.1126/sciadv.1700195. eCollection 2017, Dec. PMID:29214216 doi:https://dx.doi.org/10.1126/sciadv.1700195

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[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='5wt3' size='340' side='right'caption='[[5wt3]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5wt3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrab Pyrab]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WT3 FirstGlance]. <br>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.204&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5wt1|5wt1]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">trm5a, PYRAB01130, PAB2272 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB])</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>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine(37)-N(1))-methyltransferase tRNA (guanine(37)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.228 2.1.1.228] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5wt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wt3 OCA], [http://pdbe.org/5wt3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wt3 RCSB], [http://www.ebi.ac.uk/pdbsum/5wt3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wt3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TRM5A_PYRAB TRM5A_PYRAB]] Specifically methylates the N1 position of guanosine-37 in tRNA(Phe). In vitro, can also methylate the C7 position of 4-demethylwyosine (imG-14).<ref>PMID:20382657</ref>
+[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 ==
@@ Line 21: / Line 19: @@
 </div>
 <div class="pdbe-citations 5wt3" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]]
 == References ==
 <references/>
@@ Line 26: / Line 27: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Pyrab]]
+[[Category: Pyrococcus abyssi GE5]]
-[[Category: Jia, Q]]
+[[Category: Jia Q]]
-[[Category: Wang, C]]
+[[Category: Wang C]]
-[[Category: Xie, W]]
+[[Category: Xie W]]
-[[Category: Methyltransferase]]
-[[Category: Transferase-rna complex]]
-[[Category: Trm5a]]
-[[Category: Wyosine hypermodification]]

5wt3: Difference between revisions

Latest revision as of 16:53, 8 November 2023

Pyrococcus abyssi methyltransferase PaTrm5a bound by MTA and cognate tRNA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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