Fig. 4: Bacterial Zn²⁺-dependent deacylases share a highly conserved structural α/β-arginase/deacetylase fold.

a Ribbon representation of the catalytic cores of bacterial deacylases. For BsAcuC (2c) we show the AlphaFold2 model for the other crystal structures. All structures share a highly similar catalytic core domain (green) consisting of an eight-stranded parallel β-strand surrounded by α-helices. Additional structural features emanate from the catalytic core domain. Cluster 1 enzymes have the extended N-terminal L1-loop and an additional short C-terminal α-helix (light blue). Cluster 2 and 5 enzymes contain an extended foot pocket and additional small α-helices and loops (BsAcuC (2c): blue; VcHdaH (5b): pink). In cluster 3 enzymes the central parallel β-sheet is extended by two additional antiparallel β-strands as shown here for LpApaH (3) and by an additional pair of α-helices emanating from the core domain (red). Cluster 4 enzymes contain an extended L2-loop (PSL) (light blue). b The active site architecture in bacterial Zn²⁺-dependent deacylases is totally conserved. The active site Zn²⁺-ion (not shown here) is coordinated by two Asp-residues and a His (KpHdaH (1b): Asp181, Asp269, His183). The His acting as general base/acid (KpHdaH (1b): His144) is part of a double-His motif (KpHdaH (1b): His143, His144). Both His form charge-relay systems with two Asp or an Asp and an Asn/Gln (KpHdaH (1b): Asp179, Asn186), respectively. In agreement with eukaryotic HDACs, we found an Asn as part of the second charge-relay system in cluster 1 (KpHdaH (1b): Asn186), cluster 3 (LcApaH (3): Asn221) and cluster 4 (PsApaH (4): Asn200). c Metal ions are important for the structure and catalysis of bacterial deacylases. As their eukaryotic counterparts also bacterial deacylases use an active site Zn²⁺-ion for catalysis. Moreover, bacterial deacylases contain one or two potassium ions. Potassium ion 1 (K⁺1) is indirectly involved in catalysis while the second potassium ion, K⁺2, is a structural metal ion. Numbering is shown for KpHdaH (1b). d Bacterial deacylases exert a conserved catalytic mechanism for substrate deacylation. A catalytic base His abstracts a proton from a catalytic water molecule as a nucleophile attacking the acyl-group. A tetrahedral intermediate is formed which collapses to form the deacylated substrate. Numbering is shown for KpHdaH (1b).