Dynamics-function relationship of N-terminal acetyltransferases: the β6β7 loop modulates substrate accessibility to the catalytic site

Abstract

23 N-terminal acetyltransferases (NATs) are enzymes catalysing the transfer of the acetyl from Ac-CoA to the 24 N-terminus of proteins, one of the most common protein modifications. Unlike NATs, lysine 25 acetyltransferases (KATs) transfer an acetyl onto the amine group of internal lysines. To date, not much is 26 known on the exclusive substrate specificity of NATs towards protein N-termini. All the NATs and some 27 KATs share a common fold called GNAT. The main difference between NATs and KATs is an extra 28 hairpin loop found only in NATs called β6β7 loop. It covers the active site as a lid. The hypothesized role of 29 the loop is that of a barrier restricting the access to the catalytic site and preventing acetylation of internal 30 lysines. We investigated the dynamics-function relationships of all available structures of NATs covering 31 the three domains of life. Using elastic network models and normal mode analysis, we found a common 32 dynamics pattern conserved through the GNAT fold; a rigid V-shaped groove, formed by the β4 and β5 33 strands and three relatively more dynamic loops α1α2, β3β4 and β6β7. We identified two independent 34 dynamical domains in the GNAT fold, which is split at the β5 strand. We characterized the β6β7 hairpin 35 loop slow dynamics and show that its movements are able to significantly widen the mouth of the ligand 36 binding site thereby influencing its size and shape. Taken together our results show that NATs may have 37 access to a broader ligand specificity range than anticipated. 38Author summary 39 N-terminal acetylation concerns 80% of eukaryotic proteins and is achieved by enzymes called the 40 N-terminal acetyltransferases (NATs). They belong to the large family of acetyltransferases and 41 adopt the GNAT fold. Interestingly most lysine acetyltransferases (KATs), which acetylate 42 specifically internal lysines, share the same fold. Rationale for the ligand recognition by the GNAT 43 enzymes remains unclear. Proteins are dynamic entities that utilize their structural flexibility to 44 carry out functions in living cells. By studying the dynamics throughout the entire NATs family, 45 we found that the slow dynamics of the fold is strongly conserved. We also revealed the mobility of 46 the active site lid, namely the -hairpin loop 67, which is one of the main structural differences between 47 the NATs and the KATs. The size and shape of the ligand binding site depend on movements of that -Dynamics-function relationship of NATs 3 48 hairpin loop. We suggest that in attempts of mapping NATs specificity or ligand design the fold flexibility 49 should be taken into consideration. 50 51 Acetyltransferases are enzymes catalysing the transfer of an acetyl group from the co-factor acetyl-52 coenzyme A (Ac-CoA) to a substrate. Among them, lysine acetyltransferases (KATs) and Nα-terminal 53 acetyltransferases (NATs) perform protein acetylation to either lysine side chains or N-termini of 54 polypeptide chains, respectively. NATs acetylate 80 to 90% of the proteins of the human ...