3vyw: Difference between revisions

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[[Image:3vyw.png|left|200px]]
==Crystal structure of MNMC2 from Aquifex Aeolicus==
<StructureSection load='3vyw' size='340' side='right' caption='[[3vyw]], [[Resolution|resolution]] 2.49&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3vyw]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus_vf5 Aquifex aeolicus vf5]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2e58 2e58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VYW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VYW FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aq_1980 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 Aquifex aeolicus VF5])</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=3vyw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vyw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vyw RCSB], [http://www.ebi.ac.uk/pdbsum/3vyw PDBsum]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Posttranscriptional modifications of the wobble uridine (U34) of tRNAs play a critical role in reading NNA/G codons belonging to split codon boxes. In a subset of Escherichia coli tRNA, this wobble uridine is modified to 5-methylaminomethyluridine (mnm(5)U34) through sequential enzymatic reactions. Uridine-34 is first converted to 5-carboxymethylaminomethyluridine (cmnm(5)U34) by the MnmE/MnmG enzyme complex. The cmnm(5)U34 is further modified to mnm(5)U by the bifunctional MnmC protein. In the first reaction, the FAD-dependent oxidase domain (MnmC1) converts cmnm(5)U into 5-aminomethyluridine (nm(5)U34), and this reaction is immediately followed by the methylation of the free amine group into mnm(5)U34 by the AdoMet-dependent domain (MnmC2). Aquifex aeolicus lacks a bifunctional MnmC protein fusion, and instead encodes the Rossmann-fold protein DUF752, which is homologous to the methyltransferase MnmC2 domain of E. coli MnmC (26 % identity). Here we determined the crystal structure of the A. aeolicus DUF752 protein at 2.5 A resolution, which revealed that it catalyzes the AdoMet-dependent methylation of nm(5)U in vitro, to form mnm(5)U34 in tRNA. We also showed that naturally occurring tRNA from A. aeolicus contains the 5-mnm group attached to the C5 atom of U34. Taken together, these results support the recent proposal of an alternative MnmC1-independent shortcut pathway for producing mnm(5)U34 in tRNAs.


{{STRUCTURE_3vyw|  PDB=3vyw  |  SCENE=  }}
Characterization and structure of the Aquifex aeolicus protein DUF752: a bacterial tRNA-methyltransferase (MnmC2) functioning without the usually fused oxidase domain (MnmC1).,Kitamura A, Nishimoto M, Sengoku T, Shibata R, Jager G, Bjork GR, Grosjean H, Yokoyama S, Bessho Y J Biol Chem. 2012 Oct 22. PMID:23091054<ref>PMID:23091054</ref>


===Crystal structure of MNMC2 from Aquifex Aeolicus===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
 
== References ==
==About this Structure==
<references/>
[[3vyw]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus_vf5 Aquifex aeolicus vf5]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2e58 2e58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VYW OCA].
__TOC__
</StructureSection>
[[Category: Aquifex aeolicus vf5]]
[[Category: Aquifex aeolicus vf5]]
[[Category: Bessho, Y.]]
[[Category: Bessho, Y]]
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Structural genomic]]
[[Category: Shibata, R.]]
[[Category: Shibata, R]]
[[Category: Yokoyama, S.]]
[[Category: Yokoyama, S]]
[[Category: 2-codon set]]
[[Category: 2-codon set]]
[[Category: 5-methylaminomethyl-2-thiouridine]]
[[Category: 5-methylaminomethyl-2-thiouridine]]
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[[Category: National project on protein structural and functional analyse]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Nppsfa]]
[[Category: Nppsfa]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
[[Category: Transferase]]
[[Category: Transferase]]
[[Category: Trna wobble uridine]]
[[Category: Trna wobble uridine]]
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