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3aia

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Crystal structure of DUF358 reveals a putative SPOUT-class methltransferase

Structural highlights

3aia is a 2 chain structure with sequence from Methanocaldococcus jannaschii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.4Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 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^[3]

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

References

↑ Chatterjee K, Blaby IK, Thiaville PC, Majumder M, Grosjean H, Yuan YA, Gupta R, de Crecy-Lagard V. The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA. RNA. 2012 Mar;18(3):421-33. doi: 10.1261/rna.030841.111. Epub 2012 Jan 24. PMID:22274953 doi:http://dx.doi.org/10.1261/rna.030841.111
↑ Wurm JP, Griese M, Bahr U, Held M, Heckel A, Karas M, Soppa J, Wohnert J. Identification of the enzyme responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs. RNA. 2012 Mar;18(3):412-20. doi: 10.1261/rna.028498.111. Epub 2012 Jan 24. PMID:22274954 doi:http://dx.doi.org/10.1261/rna.028498.111
↑ Chen HY, Yuan YA. Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase. J Mol Cell Biol. 2010 Dec;2(6):366-74. PMID:21098051 doi:10.1093/jmcb/mjq034

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3aia"

Categories: Large Structures | Methanocaldococcus jannaschii | Chen HY | Yuan YA

@@ Line 3: / Line 3: @@
 <StructureSection load='3aia' size='340' side='right'caption='[[3aia]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
 == Structural highlights ==
-<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>
+<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>
-</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</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='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='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'>[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>
+[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 ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 43067]]
 [[Category: Large Structures]]
-[[Category: Chen, H Y]]
+[[Category: Methanocaldococcus jannaschii]]
-[[Category: Yuan, Y A]]
+[[Category: Chen HY]]
-[[Category: Duf358]]
+[[Category: Yuan YA]]
-[[Category: Rrna methyltransferase]]
-[[Category: Spout-class fold]]
-[[Category: Transferase]]

3aia

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Current revision

Crystal structure of DUF358 reveals a putative SPOUT-class methltransferase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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