6jp6: Difference between revisions

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 <StructureSection load='6jp6' size='340' side='right'caption='[[6jp6]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6jp6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JP6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JP6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6jp6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JP6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JP6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.699&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(cytidine(32)/guanosine(34)-2'-O)-methyltransferase tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.205 2.1.1.205] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6jp6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jp6 OCA], [http://pdbe.org/6jp6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jp6 RCSB], [http://www.ebi.ac.uk/pdbsum/6jp6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jp6 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=6jp6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jp6 OCA], [https://pdbe.org/6jp6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jp6 RCSB], [https://www.ebi.ac.uk/pdbsum/6jp6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jp6 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/WDR6_YEAST WDR6_YEAST]] Involved in regulation of Ty1 transposition. Plays also a role in the regulation of the retromer complex and is required for the recycling from endosomes of plasma membrane proteins like CAN1 and MUP1. Required together with TRM7 for the methylation of the 2'-O-ribose of nucleotides at position 34 of the tRNA anticodon loop of tRNA(Phe) and tRNA(Leu(UAA)).<ref>PMID:18202368</ref> <ref>PMID:21880895</ref> <ref>PMID:22912484</ref>  [[http://www.uniprot.org/uniprot/TRM7_YEAST TRM7_YEAST]] Methylates the 2'-O-ribose of nucleotides at positions 32 and 34 of the tRNA anticodon loop of tRNA(Phe), tRNA(Trp) and tRNA(Leu(UAA)). Requires TRM732 for methylation of the cytidine at position 32 and RTT10/TRM734 for methylation of the nucleotides at position 34 in substrate tRNAs. Lack of either of these modifications in tRNA(Phe) reduces formation of wybutosine from 1-methylguanosine at position 37.<ref>PMID:11927565</ref> <ref>PMID:22912484</ref>
+[https://www.uniprot.org/uniprot/WDR6_YEAST WDR6_YEAST] Involved in regulation of Ty1 transposition. Plays also a role in the regulation of the retromer complex and is required for the recycling from endosomes of plasma membrane proteins like CAN1 and MUP1. Required together with TRM7 for the methylation of the 2'-O-ribose of nucleotides at position 34 of the tRNA anticodon loop of tRNA(Phe) and tRNA(Leu(UAA)).<ref>PMID:18202368</ref> <ref>PMID:21880895</ref> <ref>PMID:22912484</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The complex between Trm7 and Trm734 (Trm7-Trm734) from Saccharomyces cerevisiae catalyzes 2'-O-methylation at position 34 in tRNA. We report biochemical and structural studies of the Trm7-Trm734 complex. Purified recombinant Trm7-Trm734 preferentially methylates tRNAPhe transcript variants possessing two of three factors (Cm32, m1G37 and pyrimidine34). Therefore, tRNAPhe, tRNATrp and tRNALeu are specifically methylated by Trm7-Trm734. We have solved the crystal structures of the apo and S-adenosyl-L-methionine bound forms of Trm7-Trm734. Small angle X-ray scattering reveals that Trm7-Trm734 exists as a hetero-dimer in solution. Trm7 possesses a Rossmann-fold catalytic domain, while Trm734 consists of three WD40 beta-propeller domains (termed BPA, BPB and BPC). BPA and BPC form a unique V-shaped cleft, which docks to Trm7. The C-terminal region of Trm7 is required for binding to Trm734. The D-arm of substrate tRNA is required for methylation by Trm7-Trm734. If the D-arm in tRNAPhe is docked onto the positively charged area of BPB in Trm734, the anticodon-loop is located near the catalytic pocket of Trm7. This model suggests that Trm734 is required for correct positioning of tRNA for methylation. Additionally, a point-mutation in Trm7, which is observed in FTSJ1 (human Trm7 ortholog) of nosyndromic X-linked intellectual disability patients, decreases the methylation activity.
-Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.,Hirata A, Okada K, Yoshii K, Shiraishi H, Saijo S, Yonezawa K, Shimizu N, Hori H Nucleic Acids Res. 2019 Oct 5. pii: 5581736. doi: 10.1093/nar/gkz856. PMID:31586407<ref>PMID:31586407</ref>
+==See Also==
+*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6jp6" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
-[[Category: Hirata, A]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Hori, H]]
+[[Category: Hirata A]]
-[[Category: Okada, K]]
+[[Category: Hori H]]
-[[Category: Saijo, S]]
+[[Category: Okada K]]
-[[Category: Shiraisi, H]]
+[[Category: Saijo S]]
-[[Category: Sihimzu, N]]
+[[Category: Shiraisi H]]
-[[Category: Yonezawa, K]]
+[[Category: Sihimzu N]]
-[[Category: Yoshii, K]]
+[[Category: Yonezawa K]]
-[[Category: Transferase]]
+[[Category: Yoshii K]]
-[[Category: Trna maturation]]
-[[Category: Trna methyltransferase]]