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Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB

Nature volume 597, pages 566–570 (2021)Cite this article

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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 fidelity1,2,3,4. 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 5ʹ-deoxyadenosyl 5ʹ-radical, which is responsible for removing the C2 hydrogen of the substrate5. MiaB also contains an auxiliary [Fe4S4]aux cluster, which has been implicated6,7,8,9 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 5ʹ-deoxyadenosyl 5ʹ-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.

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Fig. 1: Reactions catalysed by MTTases.
Fig. 2: RNA binding to BuMiaB.
Fig. 3: BuMiaB active site in the presence of RNA substrates.
Fig. 4: Proposed mechanism for the MiaB reaction.

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Data availability

Atomic coordinates and structure factors for the reported crystal structures in this work have been deposited to the PDB under accession numbers 7MJZ (native structure with pentasulfide bridge), 7MJY (structure with SAH and 13-mer RNA), 7MJV (structure with SAM and 17-mer RNA), 7MJX (structure with 5ʹ-dAH+Met and 13-mer RNA) and 7MJW (structure with pre-methylated BuMiaB and 5ʹ-dAH+Met and 13-mer RNA).

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Acknowledgements

This work was supported by the National Institutes of Health (NIH) (GM-122595 to S.J.B.; AI133329 to S.C.A. and T.L.G.; GM-127079 to C.K.; and GM118393, GM093342 and GM094662 to S.C.A.), the National Science Foundation (MCB-1716686 to S.J.B.), the Eberly Family Distinguished Chair in Science (S.J.B.), The Price Family Foundation (S.C.A.) and the Penn State Huck Institutes of the Life Sciences (N.H.Y.). S.J.B. is an investigator of the Howard Hughes Medical Institute. This research used resources of the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357. Use of GM/CA@APS has been funded in whole or in part with Federal funds from the National Cancer Institute (ACB-12002) and the National Institute of General Medical Sciences (AGM-12006). The Eiger 16M detector at GM/CA-XSD was funded by NIH grant S10 OD012289. Use of the LS-CAT Sector 21 was supported by the Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor (grant 085P1000817). This research also used the resources of the Berkeley Center for Structural Biology supported in part by the Howard Hughes Medical Institute. The Advanced Light Source is a Department of Energy Office of Science User Facility under contract no. DE-AC02-05CH11231. The ALS-ENABLE beamlines are supported in part by the National Institutes of Health, National Institute of General Medical Sciences, grant P30 GM124169.

Author information

Author notes

  1. Arthur J. Arcinas

    Present address: AGC Biologics, Seattle, WA, USA

Authors and Affiliations

  1. Department of Chemistry, The Pennsylvania State University, University Park, PA, USA

    Olga A. Esakova, Bo Wang, Carsten Krebs & Squire J. Booker

  2. Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA

    Tyler L. Grove & Steven C. Almo

  3. The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA

    Neela H. Yennawar

  4. Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA

    Arthur J. Arcinas, Carsten Krebs & Squire J. Booker

  5. The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, USA

    Squire J. Booker

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Contributions

O.A.E., T.L.G., N.H.Y. and S.J.B. developed the research plan and experimental strategy. O.A.E. and T.L.G. isolated and crystallized proteins and collected crystallographic data. O.A.E., B.W. and A.J.A. performed biochemical experiments. O.A.E., T.L.G., N.H.Y., S.C.A., C.K. and S.J.B. analysed and interpreted crystallographic data. O.A.E., T.L.G., N.H.Y. and S.J.B. wrote the manuscript, and all other authors reviewed and commented on it.

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Correspondence to Olga A. Esakova, Tyler L. Grove or Squire J. Booker.

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Extended data figures and tables

Extended Data Fig. 1 Comparison of BuMiaB and TmRimO structures.

a, Cartoon overlay of the structures of BuMiaB (blue) and TmRimO (PDB:4JC0) (grey). b, Electrostatic surface potential of TmRimO (blue is positive, red is negative, and grey is neutral). c, Amino acid sequence alignment of BuMiaB and TmRimO. The overall architecture of BuMiaB is similar to that of TmRimO, with RMSDs of 1.5 and 1.6 Å for the two independent RimO molecules over 324 and 329 Cαs, respectively (Table S1). In the RimO X-ray crystal structure, the two [Fe4S4] clusters are 7.3 Å apart (nearest ion in each cluster) and are connected by a pentasulfide bridge spanning the unique (non-cysteinyl-ligated) irons of each cluster. This same pentasulfide bridge is observed in the BuMiaB structure, wherein the clusters are 6.8 Å apart (see Extended Data Fig. 2a).

Extended Data Fig. 2 RNA binds to all three domains in BuMiaB.

a, Cartoon representation of the active site of BuMiaB with a pentasulfide bridge spanning the two [Fe4S4] clusters. MTTase domain, tan; radical SAM domain, grey; TRAM domain, green. b, Cartoon of BuMiaB crystallized in the presence of the 13-mer RNA substrate and 5’dAH+Met and showing the binding of the 13-mer (purple) at the interface of the three domains. c, Electrostatic surface potential (blue is positive, red is negative, and grey is neutral) indicates a positively charged active-site region promoting binding of the 13-mer. d, Conservation of amino acids in the active-site region as deduced from the CONSURF server42.

Extended Data Fig. 3 Comparison of ACSL structure in 13-mer bound to BuMiaB with that of full-length tRNAPhe bound to TmMiaA.

a, Cartoon overlay of the 13-mer (nucleotides 29-41) structure in the complex with BuMiaB and 5’-dAH+Met (purple colour), with that of Tm tRNAPhe in complex with MiaA (tan colour) (PDB ID: 2ZM5). b, Schematic diagram of hydrogen bonds formed between the 13-mer and BuMiaB.

Extended Data Fig. 4 Comparison of ACSL structure in 17-mer bound to BuMiaB with that of full-length tRNAPhe bound to TmMiaA.

a, Cartoon overlay of the 13-mer (purple colour) and 17-mer (nucleotides 27-43) (green colour) structures in complex with BuMiaB plus 5’-dAH+Met (13-mer) or BuMiaB with SAM (17-mer), with that of Tm tRNAPhe in complex with MiaA (tan colour) (PDB ID: 2ZM5). b, Schematic diagram of the H-bonds formed between the 17-mer and BuMiaB.

Extended Data Fig. 5 Active site interactions of BuMiaB with nucleotides 34 and 35 of the anticodon.

The structure of BuMiaB with the 13-mer RNA and 5’dAH+Met is shown in pink, while the structure of BuMiaB with the 17-mer RNA and SAM is shown in maroon. a, Active site interactions with G34. G34 is often modified, and its base inserts between the TRAM and RS domains in a deep cleft, which provides space for modifications. In the structure of BuMiaB in complex with 5’-dAH+Met and the 13-mer, N10 of G34 is within H-bonding distance to Ser388 of the RS domain. The 2’ and 3’ OH groups are H-bonded to two nitrogen atoms from the guanidinium group of Arg418 from the TRAM-domain. In the structure of BuMiaB with SAM and the 17-mer, the position of G34 is different, and the base no longer interacts with Ser388 and Arg418 (Extended Data Figs. 3b, 4b). b, Active site interactions with A35. In the structure of BuMiaB with 5’-dAH+Met and the 13-mer, the carboxylate oxygens of Asp319 are within H-bonding distance to N6 of A35, while the side-chain of Gln28 is in H-bonding distance to the 2’ OH of A35. The A35 base is π-stacked between Phe348 on one side and the adenine ring of i6A37 on the other. The position of A35 is shifted in the SAM-bound structure and is stabilized by π-stacking with G34 on one side and Phe348 on the other. The rotation of Phe348 supports two different orientations of A35 in the active site of the enzyme. c, Binding of i6A37 in the active site of BuMiaB in the structure with the 13-mer and 5’dAH+Met, showing that the isopentenyl group sits in a hydrophobic patch. All figures have the same colour for the domains and their associated residues: tan for MTTase, grey for radical SAM and green for TRAM.

Extended Data Fig. 6 A Model for full-length tRNA binding to BuMiaB.

a, Conservation of residues in BuMiaB as deduced from the CONSURF server. The colour code is described in the panel. b, Electrostatic surface potential, indicating positively charged regions that could stabilize tRNAPhe. c, A predicted model of interactions between the residues from the MTTase domain and the full-length tRNA.

Extended Data Fig. 7 Binding of SAM, SAH, and 5’-dAH to BuMiaB.

a, Overlay of SAM (grey), SAH (aquamarine) and 5’dAH+Met (light violet) in their complexes with BuMiaB and RNA substrates (17-mer for SAM, and 13-mer for SAH or 5’-dAH+Met). The adenine ring of SAM, SAH and 5’dAH forms face-to-face π-stacking interactions with Phe321. This stacking is further supported by edge-to-face interactions with two tyrosines (177, 352) and Phe350. N3 of the adenine ring H-bonds with the conserved Arg66 (shown in Fig. 3a), and N6 forms three H-bonds with the carbonyl groups of Ile65 (MTTase domain), and Tyr177 and Ser353 (RS domain). The ribose moiety of SAM, SAH and 5’dAH H-bonds with Arg66, Gln281 and Asp319. Methionine in the 5’dAH+Met structure or the methionine moiety of SAM (with the 17-mer RNA) and SAH (with 13-mer RNA) in structures with those molecules bound shows the canonical bidentate binding to the unique iron of the [Fe4S4]RS cluster. b, Overlay of SAM (grey) or 5’dAH+Met (light violet) in complex with BuMiaB and the 17-mer RNA (SAM) or 13-mer RNA (5’-dAH+Met). The i6A37 base is in pink for the structure with 5’dAH+Met and maroon for the structure with SAM. All figures have the same colour for the domains and their associated residues: tan for MTTase, grey for radical SAM and green for TRAM, except for Gln215 in the structure with 5’dAH+Met (panel a), which rotates.

Extended Data Fig. 8 Effect of Arg66→Gln substitution on BuMiaB activity.

a, Time course for SAH formation upon incubating 25 μM BuMiaB WT (black circles) or BuMiaB R66Q (red circles) with 1 mM SAM in the absence of dithionite. b-e, Time course for formation of SAH (b), 5’dAH (c), ms2i6A (d), and decay of i6A (e), after 30 min of initial incubation of 25 μM BuMiaB with 1 mM SAM followed by addition of 100 μM i6A ACSL RNA and reaction initiation with 1 mM dithionite. The black colour corresponds to data obtained for BuMiaB WT in the presence of the 17-mer RNA substrate; the blue colour corresponds to data obtained in the presence of the 13-mer; and the red colour corresponds to data for BuMiaB R66Q in the presence of the 17-mer. Error bars represent one standard deviation for reactions conducted in triplicate, with the centre representing the mean.

Extended Data Fig. 9 Stereoscopic representation of the active site electron density of pre-methylated BuMiaB in the presence of the 13-mer RNA substrate and 5’dAH+Met.

The structure of BuMiaB does not show any significant changes in the protein or RNA components of the complex in the pre-methylated versus non-pre-methylated states [RMSD = 0.231 Å (Cα = 371 atoms) and 0.089 Å (Cα = 439 atoms) for pre-methylated subunits A and B, respectively, versus non-pre-methylated subunit A; and 0.092 Å (Cα = 415 atoms) and 0.248 Å (Cα = 392 atoms) for pre-methylated subunits A and B, respectively, versus non-methylated subunit B]. a, The extended electron density at N3. The grey mesh corresponds to an Fo-Fc omit map for i6A contoured at 3.5σ, and the green mesh to an Fo-Fc map contoured at 3.0σ after refinement with i6A. b, The extended electron density at the sulfur atom of the [Fe3S4] cluster. The mesh corresponds to an Fo-Fc omit map for the methyl group (green colour) attached to the sulfur (grey colour) of the auxiliary cluster contoured at 3.5σ. c, In a map generated for the non-pre-methylated auxiliary cluster, no extended density is observed. The mesh corresponds to an Fo-Fc omit map for the sulfur atom of the auxiliary cluster contoured at 3.5σ. All residues have a common colour theme for the domains: tan for MTTase and grey for radical SAM.

Extended Data Table 1 X-ray crystallographic data collection and refinement statistics
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Esakova, O.A., Grove, T.L., Yennawar, N.H. et al. Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB. Nature 597, 566–570 (2021). https://doi.org/10.1038/s41586-021-03904-6

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