Structural and Enzymatic Basis for Impaired Deacylation of N-Acyl-N-Methyl Lysine Residues.
6 affiliations
- 1Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle/Saale06120, Germany.
- 2Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, Halle/Saale06120, Germany.
- 3Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, Freiburg79104, Germany.
- 4Department of Biochemistry, University of Bayreuth, Universitaetsstr. 30, Bayreuth95447, Germany.
- 5Institute of Biochemistry, University of Freiburg, Albertstr. 21, Freiburg79104, Germany.
- 6Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec252 50, Czech Republic.
Abstract
Posttranslational lysine acetylation and methylation are generally considered mutually exclusive modifications of the ε-amino group. The recent discovery of N-acetyl-N-methyl lysine (KAcMe) on histone H4 showed that both marks can coexist on the same lysine side chain, raising the question of whether this dual modification is enzymatically reversible. Here, we synthesized model peptides containing N-acyl lysine or N-acyl-N-methyl lysine residues and tested their processing by Zn2+-dependent HDACs and NAD+-dependent sirtuins. While the corresponding unmethylated substrates were deacylated by the expected enzymes, KAcMe-containing peptides were not detectably deacetylated by either enzyme family. N-methylation also blocked HDAC8/11-mediated demyristoylation and SIRT5-mediated desuccinylation, whereas SIRT2 and SIRT6 retained weak demyristoylase activity toward N-myristoyl-N-methyl lysine. X-ray crystal structures of sirtuin-peptide complexes, supported by inhibition studies and molecular docking, reveal that N-methylation disrupts productive substrate positioning and misaligns the scissile amide bond for catalysis. These findings suggest that KAcMe is resistant to canonical lysine deacetylases and may represent a persistent chromatin-associated modification.
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BibTeX
@article{hilscher2026structural,
title = {{Structural and Enzymatic Basis for Impaired Deacylation of N-Acyl-N-Methyl Lysine Residues.}},
author = {Sebastian Hilscher and Paul Horst Böttcher and Florian Friedrich and Martin Pannek and Fady Baselious and Marat Meleshin and Oliver Einsle and Cyril Barinka and Clemens Steegborn and Wolfgang Sippl and Manfred Jung and Mike Schutkowski and Cordelia Schiene-Fischer},
journal = {Biochemistry},
year = {2026},
month = oct,
doi = {10.1021/acs.biochem.6c00508},
url = {https://europepmc.org/article/MED/42917127},
note = {CC BY},
}
RIS
TY - JOUR
TI - Structural and Enzymatic Basis for Impaired Deacylation of N-Acyl-N-Methyl Lysine Residues.
AU - Sebastian Hilscher
AU - Paul Horst Böttcher
AU - Florian Friedrich
AU - Martin Pannek
AU - Fady Baselious
AU - Marat Meleshin
AU - Oliver Einsle
AU - Cyril Barinka
AU - Clemens Steegborn
AU - Wolfgang Sippl
AU - Manfred Jung
AU - Mike Schutkowski
AU - Cordelia Schiene-Fischer
PY - 2026
DA - 2026/10/01
JO - Biochemistry
DO - 10.1021/acs.biochem.6c00508
UR - https://europepmc.org/article/MED/42917127
AB - Posttranslational lysine acetylation and methylation are generally considered mutually exclusive modifications of the ε-amino group. The recent discovery of N-acetyl-N-methyl lysine (KAcMe) on histone H4 showed that both marks can coexist on the same lysine side chain, raising the question of whether this dual modification is enzymatically reversible. Here, we synthesized model peptides containing N-acyl lysine or N-acyl-N-methyl lysine residues and tested their processing by Zn2+-dependent HDACs and NAD+-dependent sirtuins. While the corresponding unmethylated substrates were deacylated by the expected enzymes, KAcMe-containing peptides were not detectably deacetylated by either enzyme family. N-methylation also blocked HDAC8/11-mediated demyristoylation and SIRT5-mediated desuccinylation, whereas SIRT2 and SIRT6 retained weak demyristoylase activity toward N-myristoyl-N-methyl lysine. X-ray crystal structures of sirtuin-peptide complexes, supported by inhibition studies and molecular docking, reveal that N-methylation disrupts productive substrate positioning and misaligns the scissile amide bond for catalysis. These findings suggest that KAcMe is resistant to canonical lysine deacetylases and may represent a persistent chromatin-associated modification.
SN - 0006-2960
SN - 1520-4995
ER -