6zmc: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 6zmc is ~~ON HOLD until Paper~~ Publication

==Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 2000 bar using the high pressure freezing method==

== Structural highlights ==

<table><tr><td colspan='2'>[[6zmc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida_KT2440 Pseudomonas putida KT2440]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZMC FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AR:ARGON'>AR</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6zmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zmc OCA], [https://pdbe.org/6zmc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zmc RCSB], [https://www.ebi.ac.uk/pdbsum/6zmc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zmc ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/A0A179QS89_PSEPU A0A179QS89_PSEPU]

== 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.

~~Authors~~:

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>

~~Description~~:

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

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Pseudomonas putida KT2440]]

[[Category: Atta M]]

[[Category: Carpentier P]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6zmc is ON HOLD  until Paper Publication
+==Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 2000 bar using the high pressure freezing method==
+<StructureSection load='6zmc' size='340' side='right'caption='[[6zmc]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6zmc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida_KT2440 Pseudomonas putida KT2440]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZMC FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AR:ARGON'>AR</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6zmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zmc OCA], [https://pdbe.org/6zmc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zmc RCSB], [https://www.ebi.ac.uk/pdbsum/6zmc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zmc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A179QS89_PSEPU A0A179QS89_PSEPU]
+<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.
-Authors:
+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>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6zmc" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Pseudomonas putida KT2440]]
+[[Category: Atta M]]
+[[Category: Carpentier P]]