SNAP output for PDB entry 7mjv [SNAP web server]

PDB-id

7mjv; SNAP-derived features in text and JSON formats; DNAproDB

Class

transferase-RNA

Method

X-ray (2.24 Å)

Summary

Miab in the complex with s-adenosylmethionine and RNA

Reference

Esakova OA, Grove TL, Yennawar NH, Arcinas AJ, Wang B, Krebs C, Almo SC, Booker SJ (2021): "Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB." Nature, 597, 566-570. doi: 10.1038/s41586-021-03904-6.

Abstract

Numerous post-transcriptional modifications of transfer RNAs have vital roles in translation. The 2-methylthio-N₆-isopentenyladenosine (ms₂i₆A) modification occurs at position 37 (A37) in transfer RNAs that contain adenine in position 36 of the anticodon, and serves to promote efficient A:U codon-anticodon base-pairing and to prevent unintended base pairing by near cognates, thus enhancing translational fidelity_1-4. The ms₂i₆A modification is installed onto isopentenyladenosine (i₆A) by MiaB, a radical S-adenosylmethionine (SAM) methylthiotransferase. As a radical SAM protein, MiaB contains one [Fe₄S₄]_RS cluster used in the reductive cleavage of SAM to form a 5'-deoxyadenosyl 5'-radical, which is responsible for removing the C₂ hydrogen of the substrate₅. MiaB also contains an auxiliary [Fe₄S₄]_aux cluster, which has been implicated_6-9 in sulfur transfer to C₂ of i₆A37. How this transfer takes place is largely unknown. Here we present several structures of MiaB from Bacteroides uniformis. These structures are consistent with a two-step mechanism, in which one molecule of SAM is first used to methylate a bridging µ-sulfido ion of the auxiliary cluster. In the second step, a second SAM molecule is cleaved to a 5'-deoxyadenosyl 5'-radical, which abstracts the C₂ hydrogen of the substrate but only after C₂ has undergone rehybridization from sp₂ to sp₃. This work advances our understanding of how enzymes functionalize inert C-H bonds with sulfur.