3aia: Difference between revisions
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==Crystal structure of DUF358 reveals a putative SPOUT-class methltransferase== | ==Crystal structure of DUF358 reveals a putative SPOUT-class methltransferase== | ||
<StructureSection load='3aia' size='340' side='right' caption='[[3aia]], [[Resolution|resolution]] 1.40Å' scene=''> | <StructureSection load='3aia' size='340' side='right'caption='[[3aia]], [[Resolution|resolution]] 1.40Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3aia]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3aia]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AIA FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PBL:PENTANE-2,2,4,4-TETROL'>PBL</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PBL:PENTANE-2,2,4,4-TETROL'>PBL</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ai9|3ai9]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ai9|3ai9]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MJ1640 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MJ1640 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3aia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aia OCA], [https://pdbe.org/3aia PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3aia RCSB], [https://www.ebi.ac.uk/pdbsum/3aia PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3aia ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/TRMY_METJA TRMY_METJA]] Specifically catalyzes the N1-methylation of pseudouridine at position 54 (Psi54) in tRNAs.[HAMAP-Rule:MF_00587]<ref>PMID:22274953</ref> <ref>PMID:22274954</ref> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Atcc 43067]] | [[Category: Atcc 43067]] | ||
[[Category: Large Structures]] | |||
[[Category: Chen, H Y]] | [[Category: Chen, H Y]] | ||
[[Category: Yuan, Y A]] | [[Category: Yuan, Y A]] | ||
Revision as of 17:53, 29 December 2021
Crystal structure of DUF358 reveals a putative SPOUT-class methltransferaseCrystal structure of DUF358 reveals a putative SPOUT-class methltransferase
Structural highlights
Function[TRMY_METJA] Specifically catalyzes the N1-methylation of pseudouridine at position 54 (Psi54) in tRNAs.[HAMAP-Rule:MF_00587][1] [2] Publication Abstract from PubMedThe proteins in DUF358 family are all bacterial proteins, which are approximately 200 amino acids long with unknown function. Bioinformatics analysis suggests that these proteins contain several conserved arginines and aspartates that might adopt SPOUT-class fold. Here we report crystal structure of Methanocaldococcus jannaschii DUF358/Mj1640 in complex with S-adenosyl-L-methionine (SAM) at 1.4 A resolution. The structure reveals a single domain structure consisting of eight-stranded beta-sheets sandwiched by six alpha-helices at both sides. Similar to other SPOUT-class members, Mj1640 contains a typical deep trefoil knot at its C-terminus to accommodate the SAM cofactor. However, Mj1640 has limited structural extension at its N-terminus, which is unique to this family member. Mj1640 forms a dimer, which is mediated by two parallel pairs of alpha-helices oriented almost perpendicular to each other. Although Mj1640 shares close structural similarity with Nep1, the significant differences in N-terminal extension domain and the overall surface charge distribution strongly suggest that Mj1640 might target a different RNA sequence. Detailed structural analysis of the SAM-binding pocket reveals that Asp157 or Glu183 from its own monomer or Ser43 from the associate monomer probably plays the catalytic role for RNA methylation. Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase.,Chen HY, Yuan YA J Mol Cell Biol. 2010 Dec;2(6):366-74. PMID:21098051[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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