3aia: Difference between revisions
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< | ==Crystal structure of DUF358 reveals a putative SPOUT-class methltransferase== | ||
<StructureSection load='3aia' size='340' side='right'caption='[[3aia]], [[Resolution|resolution]] 1.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3aia]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. 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> | |||
or | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4Å</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='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> | |||
== 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;"> | |||
== Publication Abstract from PubMed == | |||
The 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<ref>PMID:21098051</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3aia" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
== | |||
< | |||
[[Category: Methanocaldococcus jannaschii]] | [[Category: Methanocaldococcus jannaschii]] | ||
[[Category: Chen | [[Category: Chen HY]] | ||
[[Category: Yuan | [[Category: Yuan YA]] | ||
Latest revision as of 18:46, 4 October 2023
Crystal structure of DUF358 reveals a putative SPOUT-class methltransferaseCrystal structure of DUF358 reveals a putative SPOUT-class methltransferase
Structural highlights
FunctionTRMY_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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