6zma
From Proteopedia
(Difference between revisions)
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==Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 140 bar of krypton using the soak and freeze methodology== | ==Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 140 bar of krypton using the soak and freeze methodology== | ||
| - | <StructureSection load='6zma' size='340' side='right'caption='[[6zma]]' scene=''> | + | <StructureSection load='6zma' size='340' side='right'caption='[[6zma]], [[Resolution|resolution]] 2.15Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZMA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZMA FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6zma]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZMA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZMA FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zma OCA], [http://pdbe.org/6zma PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zma RCSB], [http://www.ebi.ac.uk/pdbsum/6zma PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zma ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=KR:KRYPTON'>KR</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AYO08_21560, CBL13_00280, CBP06_18695 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zma OCA], [http://pdbe.org/6zma PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zma RCSB], [http://www.ebi.ac.uk/pdbsum/6zma PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zma ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | MiaE (2-methylthio-N6-isopentenyl-adenosine37-tRNA monooxygenase) is a unique non-heme diiron enzyme that catalyzes the O2-dependent post-transcriptional allylic hydroxylation of a hypermodified nucleotide 2-methylthio-N6-isopentenyl-adenosine (ms2i6A37) at position 37 of selected tRNA molecules to produce 2-methylthio-N6-4-hydroxyisopentenyl-adenosine (ms2io6A37). Here, we report the in vivo activity, biochemical, spectroscopic characterization and X-ray crystal structure of MiaE from Pseudomonas putida. The investigation demonstrates that the putative pp-2188 gene encodes a MiaE enzyme. The structure shows that Pp-MiaE consists of a catalytic diiron(III) domain with a four alpha-helix bundle fold. A docking model of Pp-MiaE in complex with tRNA, combined with site directed mutagenesis and in vivo activity shed light on the importance of an additional linker region for substrate tRNA recognition. Finally, krypton-pressurized Pp-MiaE experiments, revealed the presence of defined O2 site along a conserved hydrophobic tunnel leading to the diiron active center. | ||
| + | |||
| + | Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction.,Carpentier P, Lepretre C, Basset C, Douki T, Torelli S, Duarte V, Hamdane D, Fontecave M, Atta M Nucleic Acids Res. 2020 Aug 12. pii: 5891576. doi: 10.1093/nar/gkaa667. PMID:32785618<ref>PMID:32785618</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6zma" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Bacillus fluorescens putidus flugge 1886]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Atta M]] | + | [[Category: Atta, M]] |
| - | [[Category: Carpentier P]] | + | [[Category: Carpentier, P]] |
| + | [[Category: Oxidoreductase]] | ||
| + | [[Category: Trna-monooxygenase metallo-enzyme trna-modifying enzyme hydroxylase]] | ||
Revision as of 06:42, 7 October 2020
Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 140 bar of krypton using the soak and freeze methodology
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