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Kinetic control of nascent protein biogenesis by peptide deformylase

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Bögeholz,  Lena A. K.
Department of Physical Biochemistry, MPI for biophysical chemistry, Max Planck Society;

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Mercier,  Evan
Department of Physical Biochemistry, MPI for biophysical chemistry, Max Planck Society;

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Wintermeyer,  Wolfgang
Department of Physical Biochemistry, MPI for biophysical chemistry, Max Planck Society;

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Rodnina,  Marina V.       
Department of Physical Biochemistry, MPI for biophysical chemistry, Max Planck Society;

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s41598-021-03969-3.pdf
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Citation

Bögeholz, L. A. K., Mercier, E., Wintermeyer, W., & Rodnina, M. V. (2021). Kinetic control of nascent protein biogenesis by peptide deformylase. Scientific Reports, 11: 24457. doi:0.1038/s41598-021-03969-3.


Cite as: https://hdl.handle.net/21.11116/0000-000C-A855-7
Abstract
Synthesis of bacterial proteins on the ribosome starts with a formylated methionine. Removal of the N-terminal formyl group is essential and is carried out by peptide deformylase (PDF). Deformylation occurs co-translationally, shortly after the nascent-chain emerges from the ribosomal exit tunnel, and is necessary to allow for further N-terminal processing. Here we describe the kinetic mechanism of deformylation by PDF of ribosome-bound nascent-chains and show that PDF binding to and dissociation from ribosomes is rapid, allowing for efficient scanning of formylated substrates in the cell. The rate-limiting step in the PDF mechanism is a conformational rearrangement of the nascent-chain that takes place after cleavage of the formyl group. Under conditions of ongoing translation, the nascent-chain is deformylated rapidly as soon as it becomes accessible to PDF. Following deformylation, the enzyme is slow in releasing the deformylated nascent-chain, thereby delaying further processing and potentially acting as an early chaperone that protects short nascent chains before they reach a length sufficient to recruit other protein biogenesis factors.