4yvi: Difference between revisions

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-'''Unreleased structure'''
-The entry 4yvi is ON HOLD  until Paper Publication
+==Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA==
+<StructureSection load='4yvi' size='340' side='right'caption='[[4yvi]], [[Resolution|resolution]] 3.01&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4yvi]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae_Rd_KW20 Haemophilus influenzae Rd KW20] and [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YVI 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]] 3.01&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SFG:SINEFUNGIN'>SFG</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=4yvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yvi OCA], [https://pdbe.org/4yvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yvi RCSB], [https://www.ebi.ac.uk/pdbsum/4yvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yvi ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRMD_HAEIN TRMD_HAEIN] Specifically methylates guanosine-37 in various tRNAs (By similarity).[HAMAP-Rule:MF_00605]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life. In bacteria, TrmD catalyzes the N(1)-methylguanosine (m(1)G) modification at position 37 in transfer RNAs (tRNAs) with the (36)GG(37) sequence, using S-adenosyl-l-methionine (AdoMet) as the methyl donor. The m(1)G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome. Here we report the crystal structure of the TrmD homodimer in complex with a substrate tRNA and an AdoMet analog. Our structural analysis revealed the mechanism by which TrmD binds the substrate tRNA in an AdoMet-dependent manner. The trefoil-knot center, which is structurally conserved among SPOUT MTases, accommodates the adenosine moiety of AdoMet by loosening/retightening of the knot. The TrmD-specific regions surrounding the trefoil knot recognize the methionine moiety of AdoMet, and thereby establish the entire TrmD structure for global interactions with tRNA and sequential and specific accommodations of G37 and G36, resulting in the synthesis of m(1)G37-tRNA.
-Authors: Yoshida, K., Ito, T., Yokoyama, S.
+Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.,Ito T, Masuda I, Yoshida K, Goto-Ito S, Sekine S, Suh SW, Hou YM, Yokoyama S Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):E4197-205. doi:, 10.1073/pnas.1422981112. Epub 2015 Jul 16. PMID:26183229<ref>PMID:26183229</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Yoshida, K]]
+<div class="pdbe-citations 4yvi" style="background-color:#fffaf0;"></div>
-[[Category: Ito, T]]
-[[Category: Yokoyama, S]]
+==See Also==
+*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Haemophilus influenzae Rd KW20]]
+[[Category: Large Structures]]
+[[Category: Thermotoga maritima MSB8]]
+[[Category: Ito T]]
+[[Category: Yokoyama S]]
+[[Category: Yoshida K]]