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bioRxiv · 10.1101/2024.11.29.625835

Cryo-EM structures of the MnmE-MnmG complex reveal large conformational changes and provide new insights into the mechanism of tRNA modification

Maes, L.·Martin, E.·Bickel, D.·Claeys, S.·Vranken, W. F.·Fislage, M.·Galicia, C.·Versees, W.
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Abstract

MnmE and MnmG form a conserved protein complex responsible for the addition of a 5-carboxymethylaminomethyl (cmnm5) group onto the wobble uridine of several tRNAs. Within this complex, both proteins collaborate intensively to catalyze a tRNA modification reaction that involves glycine as a substrate in addition to three different cofactors, with FAD and NADH binding to MnmG and methylenetetrahydrofolate (5,10-CH2-THF) to MnmE. Without structures of the MnmEG complex it remained enigmatic how these substrates and co-factors can be brought together in a concerted manner. Prior SAXS data suggested that the MnmE (2) and MnmG ({beta}2) homodimers can adopt either an 2{beta}2 or 4{beta}2 complex, depending on the nucleotide state of MnmE. Here, we report the cryo-EM structures of the MnmEG complex in the 2{beta}2 and 4{beta}2 oligomeric states. These structures reveal that MnmE undergoes large conformational changes upon interaction with MnmG, resulting in an asymmetric MnmE dimer. In particular, the functionally important C-terminal helix of MnmE relocates from the 5,10-CH2-THF binding pocket of MnmE to the FAD binding pocket of MnmG, thus suggesting a mechanism for the transfer of an activated methylene group from one active site to the other. Together, these findings provide crucial new insights into the MnmEG-catalyzed reaction. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/625835v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@144e41forg.highwire.dtl.DTLVardef@1dce537org.highwire.dtl.DTLVardef@14c9359org.highwire.dtl.DTLVardef@5dec04_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Maes, L., Martin, E., Bickel, D., Claeys, S., Vranken, W. F., Fislage, M., Galicia, C., Versees, W.. 2024-11-30. Cryo-EM structures of the MnmE-MnmG complex reveal large conformational changes and provide new insights into the mechanism of tRNA modification. https://doi.org/10.1101/2024.11.29.625835

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