Lysine malonylation (Kmal, maK), protein malonylation or malonylation, is a reversible post-translational modification (PTM) in eukaryotic and prokaryotic cells, in which a malonyl group (–CO–CH2–COOH) is added to a lysine (K) residue of a protein. It was first identified in 2011 by Peng et al. as an evolutionarily conserved modification and belongs to the acidic acyl modifications such as succinylation and glutarylation. As a dynamically regulated modification, it responds to conditions such as stress responses, metabolic processes, and mutations, thereby influencing the charge, structure, and function of proteins. This involves, among other things, the metabolic pathways of glucose and fatty acids as well as histone-mediated gene regulation, and is increasingly associated with immune regulation, angiogenesis, osteoarthritis, cancer and metabolic diseases such as obesity and type 2 diabetes. Its biological significance is increasingly recognized, but many aspects of its regulation and function remain unresolved, so that its therapeutic potential is still unexplored.

At physiological pH, the ε-amino group (–NH₂) of the lysine residue exists almost entirely in its protonated form (–NH₃⁺), whereas the carboxyl group (–COOH) of the malonyl group exists almost entirely in its deprotonated form (–COO^-). Through the covalent attachment of a malonyl group to the ε-amino group, the lysine residue loses its positive charge and assumes the negative charge of the malonyl group, resulting in a charge shift from +1 to −1. This complete reversal of charge is thought to disrupt ionic interactions both within the protein itself and with negatively charged components of nucleotides, proteins and small molecules. Such alterations can occur at multiple lysine residues within a single protein, although their overall frequency varies considerably across the proteome. In mouse liver, for example, about half of all malonylated proteins contain a single site, while the frequency decreases sharply beyond four sites and only a few are extensively modified, the most heavily modified enzyme being carbamoyl‑phosphate synthetase 1 (CPS1) of the urea cycle with 31 sites.

In the context of other lysine acylations, malonylation can be positioned as follows:

While acetylation neutralizes lysine's positive charge, malonylation introduces a negative one, placing it among the acidic acylations alongside methylmalonylation, succinylation, glutarylation, 3‑hydroxy‑3‑methylglutarylation, 3‑methylglutaconylation, and 3‑methylglutarylation. In size, malonylation (three carbons) is bulkier than acetylation (two) but smaller than succinylation (four) and glutarylation (five). As a result, such acidic acyl modifications, as discussed for malonylation and succinylation, are expected to exert a greater impact than acetylation at the same lysine site.

Each modification arises from the corresponding acyl-CoA derivative. Malonyl‑CoA is produced in cytosol and mitochondria by acetyl‑CoA carboxylase (ACC) and, in mitochondria, also by acyl-CoA synthetase family member 3 (ACSF3); succinyl‑CoA stems from the TCA cycle and amino acid catabolism; glutaryl‑CoA from amino acid catabolism; and methylmalonyl‑CoA from amino acid and odd‑chain fatty acid metabolism, which accumulates in vitamin B12 deficiency and methylmalonic acidemias. Malonyl‑CoA is far less reactive toward proteins than succinyl‑CoA or glutaryl‑CoA because, like acetyl‑CoA, its shorter carbon chain cannot support the intramolecular catalysis needed to form a reactive cyclic anhydride intermediate, which in turn enables modification over a broader pH range. Malonyl, succinyl, and glutaryl groups are removed by Sirtuin 5 (SIRT5), which shows little activity toward acetylation.

Malonylation occurs mainly in mitochondria but also in the cytosol and nucleus. In mouse liver, about 60% of malonylated proteins are mitochondrial, whereas in human fibroblasts the distribution is more even. Succinylation and glutarylation are likewise enriched in mitochondria but not exclusive to them. The relative abundance of these modifications reflects acyl-CoA availability: acetylation is most common, succinylation reaches 10–30 % of acetylation levels, malonylation is at least tenfold less frequent, and glutarylation occurs only in trace amounts. In addition to their differing frequencies, malonylation, succinylation, and acetylation can also target the same lysine site. In mouse liver mitochondria, about 85 % of succinylation sites overlap with at least one of these modifications, and ~6 % can contain all three, mainly in proteins involved in fatty acid oxidation, glutaryl-CoA degradation, and ketogenesis. In contrast, only 55 % of malonylation sites overlap with succinylation, while about 45 % are unique. These distinct patterns suggest a specific regulatory role for malonylation among lysine acyl modifications.

Malonyl-CoA, the donor for lysine malonylation, cannot cross membranes and must be synthesized locally in each cellular compartment.

The extent of malonylation increases with malonyl‑CoA availability particularly under conditions such as metabolic stress or enzyme deficiencies, for example malonyl‑CoA decarboxylase deficiency.