6zmc: Difference between revisions

Latest revision as of 11:54, 1 February 2024

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

Structural highlights

6zmc is a 2 chain structure with sequence from Pseudomonas putida KT2440. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	AR, CA, CL, FE, PEG, PG4, TRS
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

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^[1]

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

References

↑ Carpentier P, Lepretre C, Basset C, Douki T, Torelli S, Duarte V, Hamdane D, Fontecave M, Atta M. Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction. Nucleic Acids Res. 2020 Aug 12. pii: 5891576. doi: 10.1093/nar/gkaa667. PMID:32785618 doi:https://dx.doi.org/10.1093/nar/gkaa667

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Carpentier P, Lepretre C, Basset C, Douki T, Torelli S, Duarte V, Hamdane D, Fontecave M, Atta M. Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction. Nucleic Acids Res. 2020 Aug 12. pii: 5891576. doi: 10.1093/nar/gkaa667. PMID:32785618 doi:https://dx.doi.org/10.1093/nar/gkaa667

[1]

@@ Line 3: / Line 3: @@
 <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 [http://en.wikipedia.org/wiki/Psepk Psepk]. 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 [http://proteopedia.org/fgij/fg.htm?mol=6ZMC FirstGlance]. <br>
+<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='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>
+</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='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=160488 PSEPK])</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'>[http://proteopedia.org/fgij/fg.htm?mol=6zmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zmc OCA], [http://pdbe.org/6zmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zmc RCSB], [http://www.ebi.ac.uk/pdbsum/6zmc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zmc ProSAT]</span></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 ==
@@ Line 22: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Psepk]]
+[[Category: Pseudomonas putida KT2440]]
-[[Category: Atta, M]]
+[[Category: Atta M]]
-[[Category: Carpentier, P]]
+[[Category: Carpentier P]]
-[[Category: Oxidoreductase]]
-[[Category: Trna-monooxygenase metallo-enzyme trna-modifying enzyme hydroxylase]]

6zmc: Difference between revisions

Latest revision as of 11:54, 1 February 2024

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

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools