Structure of the eukaryotic protein O-mannosyltransferase Pmt1−Pmt2 complex

Abstract

In eukaryotes, a nascent peptide entering the endoplasmic reticulum (ER) is scanned by two Sec61 translocon-associated large membrane machines for protein N-glycosylation and protein O-mannosylation, respectively. While the structure of the eight-protein oligosaccharyltransferase complex has been determined recently, the structures of mannosyltransferases of the PMT family, which are an integral part of ER protein homeostasis, are still unknown. Here we report cryo-EM structures of the Saccharomyces cerevisiae Pmt1−Pmt2 complex bound to a donor and an acceptor peptide at 3.2-Å resolution, showing that each subunit contains 11 transmembrane helices and a lumenal β-trefoil fold termed the MIR domain. The structures reveal the substrate recognition model and confirm an inverting mannosyl-transferring reaction mechanism by the enzyme complex. Furthermore, we found that the transmembrane domains of Pmt1 and Pmt2 share a structural fold with the catalytic subunits of oligosaccharyltransferases, confirming a previously proposed evolutionary relationship between protein O-mannosylation and protein N-glycosylation.

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Fig. 1: Structure of the yeast Pmt1−Pmt2 complex.
Fig. 2: The interfaces between Pmt1 and Pmt2.
Fig. 3: The active site of the Pmt1−Pmt2 complex.
Fig. 4: Superimposition of the transmembrane domain of Pmt1 (green) with that of the PglB structure (gray).
Fig. 5: Mapping of the congenital muscular dystrophy mutations found in human POMT1−POMT2 onto the structure of the yeast Pmt1−Pmt2.

Data availability

The cryo-EM 3D maps of the S. cerevisiae Pmt1–Pmt2 alone or complexed with the acceptor peptide have been deposited at the EMDB database with accession codes EMD-20240 and EMD-20236, respectively. Their corresponding atomic models were deposited at the RCSB PDB with accession codes 6P2R and 6P25, respectively. The crystal structure of the Pmt2 MIR domain was deposited at the RCSB PDB with accession code 6P28.

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Acknowledgements

We thank G. Li for advice on constructing yeast strains and D. Nadziejka for critical reading of the manuscript. Cryo-EM data were collected at the David Van Andel Advanced Cryo-Electron Microscopy Suite at Van Andel Research Institute. We thank G. Zhao and X. Meng for assistance in data collection. This work was supported by the U.S. National Institutes of Health grant no. R01 CA231466 (to H.L.). X-ray diffraction data were collected at the Life Sciences Collaborative Access Team (LS-CAT) beamline at the Advanced Photon Source, which was supported by the Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor (Grant no. 085P1000817).

Author information

L.B. and H.L. designed experiments. L.B. carried out most of the experiments. A. Kovach, Q.Y. and A. Kenny participated in sample preparation. L.B. and H.L. analyzed the data and wrote the manuscript.

Correspondence to Huilin Li.

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Peer review information: Katarzyna Marcinkiewicz was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Integrated supplementary information

Supplementary Figure 1 Cryo-EM 3D density map of the Pmt1−Pmt2−peptide complex and comparison with 3D map of the Pmt1−Pmt2 complex.

(A) 3D map of the Pmt1Pmt2peptide complex surface-rendered and shown in a front, a back, a top, and a side-on view. Light green shows the transmembrane region of Pmt1; green, the MIR domain of Pmt1; purple-blue, the transmembrane region of Pmt2; and purple, the MIR domain of Pmt2. Sugar donor and peptide acceptor are orange and orange-red, respectively. The two N-glycans and three phospholipids are in red and gray, respectively. (B) 3D map of the as-purified Pmt1–Pmt2 complex is surface-rendered and shown as gray in a top view. (C) Surface-rendered 3D map of the Pmt1–Pmt2–peptide shown in yellow and in the same top view as in (B). (D) The two 3D maps are superimposed and shown in the same top view as in (A). (E) Zoomed views of the areas in the black and orange squares in (B) and (C), respectively. The extra density from the model acceptor peptide is orange-red in (C) and (D). The surface-rendering threshold in (E) is slightly lower than those used in (B-D), to show the continuous peptide density.

Supplementary Figure 2

3D density map and atomic model of selected regions in the structure of the Pmt1–Pmt2–peptide complex.

Supplementary Figure 3 Crystal structure of the MIR domain of Pmt2.

(A) Gel filtration of the MIR domain of Pmt2. The inset shows the SDS-PAGE gel of the five fractions collected around the filtration peak (shown by the horizontal arrow). (B) 3D electron density map and atomic model of a selected region. (C) Overall structure of the MIR domain of Pmt2 shown in a top, bottom, and side views. The structure contains three repeats of the MIR motif, each of which has four β-strands and one short α-helix. The numbers refer to the β-strand number in the β-trefoil fold. All residues in the Pmt2 MIR domain (amino acids 337-532) are resolved (i.e., no residues are missing in the crystal structure).

Supplementary Figure 4 Superposition of Pmt1 and Pmt2 structures.

(A) Superposition of the transmembrane regions of Pmt1 (green) and Pmt2 (purple). Dol-P in Pmt1 is in orange sticks, and the acceptor peptide in Pmt2 is in red spheres. (B) Superposition of the MIR domains of Pmt1 (green) and Pmt2 (purple). (C) Superposition of Pmt1 and Pmt2, aligned by their transmembrane regions, showing the displaced orientation and location of their respective MIR domains. Pmt1 is show in green carton and as a transparent green surface. Pmt2 is shown only in blue for clarity. The curved arrow indicates the relative movement of about 13 Å and rotation of about 17° between the MIR domains of Pmt1 and Pmt2.

Supplementary Figure 5 Comparison of the Dol-P binding site in S. cerevisiae Pmt1−Pmt2 complex (A) with the donor binding site in the archaeal Pyrococcus furiosus DPMS (B) and superposition of the MIR domain of Pmt2 (purple) and the sugar-bound lectin (salmon) (C).

(A) A close-up view of the active site of Pmt1. The phosphate group of the donor Dol-P-Man is marked by a yellow asterisk. The mannose is missing in our density map; but its likely position is shown as a dashed red hexagon. (B) A close-up view of the active site of the product (Dol-P-Man) bound DPMS structure (PDB 5MM1). The phosphate group of Dol-P is marked by a yellow asterisk. (C) The lectin (PDB ID 2IHO) has an N-terminal β-trefoil fold domain and a C-terminal dimerization domain. The lectin structure is in complex with the trisaccharide Gal(1,3)Gal(1,4)GlcNAc. For clarity, only the β-trefoil fold bound to the sugar (in red spheres) is shown. The Dol-P bound to the Pmt1 (green) is also shown in red spheres.

Supplementary information

Supplementary Information

Supplementary Figs. 1–5, Supplementary Table 1 and Supplementary Notes 1–4

Reporting Summary

Supplementary Video 1

Cryo-EM 3D density map of Pmt1−Pmt2−acceptor peptide is rotated 360°, first around a vertical axis, followed up another 360° rotation around a horizontal axis. The Pmt1 density is in green and Pmt2 is in purple. Their respective MIR domains are a slightly stronger shade. The product density Dol-P is orange, and the two glycans are red.

Supplementary Video 2

Nutation of the active site of Pmt1. Pmt1 is in green, the model acceptor peptide in red and Dol-P in orange. Key residues in the active site are shown as sticks

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