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A peptide deformylase–ribosome complex reveals mechanism of nascent chain processing

Abstract

Messenger-RNA-directed protein synthesis is accomplished by the ribosome1,2,3. In eubacteria, this complex process is initiated by a specialized transfer RNA charged with formylmethionine (tRNAfMet)4,5,6. The amino-terminal formylated methionine of all bacterial nascent polypeptides blocks the reactive amino group to prevent unfavourable side-reactions and to enhance the efficiency of translation initiation7,8. The first enzymatic factor that processes nascent chains is peptide deformylase (PDF)5,9,10,11; it removes this formyl group as polypeptides emerge from the ribosomal tunnel12,13 and before the newly synthesized proteins can adopt their native fold, which may bury the N terminus. Next, the N-terminal methionine is excised by methionine aminopeptidase14. Bacterial PDFs are metalloproteases sharing a conserved N-terminal catalytic domain. All Gram-negative bacteria, including Escherichia coli, possess class-1 PDFs characterized by a carboxy-terminal α-helical extension15. Studies focusing on PDF as a target for antibacterial drugs14,16 have not revealed the mechanism of its co-translational mode of action despite indications in early work that it co-purifies with ribosomes17. Here we provide biochemical evidence that E. coli PDF interacts directly with the ribosome via its C-terminal extension. Crystallographic analysis of the complex between the ribosome-interacting helix of PDF and the ribosome at 3.7 Å resolution reveals that the enzyme orients its active site towards the ribosomal tunnel exit for efficient co-translational processing of emerging nascent chains. Furthermore, we have found that the interaction of PDF with the ribosome enhances cell viability. These results provide the structural basis for understanding the coupling between protein synthesis and enzymatic processing of nascent chains, and offer insights into the interplay of PDF with the ribosome-associated chaperone trigger factor.

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Figure 1: PDF specifically binds to the 50S ribosomal subunit via its C-terminal helix.
Figure 2: Interaction of the C-terminal helix of PDF with the ribosome.
Figure 3: Growth analysis comparing the in vivo complementation abilities of PDF and PDFΔCII.
Figure 4: Model for the concerted mechanism of PDF and trigger factor.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors of the 70S–PDF complex have been deposited in the Protein Data Bank under accession codes 2VHM, 2VHN, 2VHO and 2VHP.

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Acknowledgements

Crystallographic data were collected at the beamline X06SA at the Swiss Light Source (SLS). We are grateful to C. Schulze-Briese, S. Gutmann, E. Pohl, S. Russo and T. Tomizaki for their outstanding support at the SLS. We thank B. Mikolasek for ribosome preparation, F. Parmeggiani and A. Plückthun at the University of Zurich for assistance with the surface plasmon resonance measurements and access to the Biacore 3000 instrument, R. Brunisholz at the Functional Genomics Center Zurich for mass-spectrometric analysis, D. Böhringer, J. Erzberger, S. Jenni and M. Müller for critically reading the manuscript and all members of the Ban laboratory for suggestions and discussions. This work was supported by the Swiss National Science Foundation (SNSF) and the National Center of Excellence in Research (NCCR) Structural Biology programme of the SNSF.

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Correspondence to Nenad Ban.

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The file contains Supplementary Results, Supplementary Figures 1-6 with Legends, Supplementary Tables 1-2 and additional references. (PDF 3323 kb)

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Bingel-Erlenmeyer, R., Kohler, R., Kramer, G. et al. A peptide deformylase–ribosome complex reveals mechanism of nascent chain processing. Nature 452, 108–111 (2008). https://doi.org/10.1038/nature06683

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