6ZMB

Structure of the native tRNA-Monooxygenase enzyme MiaE

Summary for 6ZMB

• Entry DOI: 10.2210/pdb6zmb/pdb
• Descriptor: tRNA hydroxylase, FE (III) ION, CHLORIDE ION, ... (10 entities in total)
• Functional Keywords: trna-monooxygenase metallo-enzyme trna-modifying enzyme hydroxylase, oxidoreductase
• Biological source: Pseudomonas putida KT2440
• Total number of polymer chains: 2
• Total formula weight: 46873.95

Authors

Carpentier, P.,Atta, M. (deposition date: 2020-07-02, release date: 2020-09-02, Last modification date: 2024-01-31)

Primary citation

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., 48:9918-9930, 2020

PubMed Abstract: 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.

PubMed: 32785618
DOI: 10.1093/nar/gkaa667

Experimental method

X-RAY DIFFRACTION (1.7 Å)