Fig. 7: Structural features of cluster 4 containing polyamine deacetylases.
From: Distribution and diversity of classical deacylases in bacteria
a The structure of PsApaH (4) confirms cluster 4 enzymes forming head-to-head dimers. Dimer formation proceeds via two structural features, i.e. an extended L2-loop (PSL, red) and the N-terminal L1-loop forming a two-stranded β-hairpin (yellow). The L1-loop was not resolved in the PsApaH (4) apo structure. Comparison with the structure of M. ramosa•N8-acetylspermidine (PDB: 3Q9C) suggests an induced fit mechanism upon substrate binding stabilizing the L1-loop. Dimer formation is mediated by interactions such as the salt bridge between Arg95 of the PSL-loop of monomer 1 (M1) and Asp163 of monomer 2 (M2). b Superposition of the structure of PsApaH (4) and the structure of M. ramosa ApaH (4) in complex with N8-acetylspermidine reveals molecular mechanisms of substrate specificity. The L1-loop mediates dimer formation and forms a lid of the active site in cis limiting active site access of the substrate also in trans, i.e. for the other monomer. The selectivity for N8-acetylspermidine compared to N1-acetylspermidine is created by M. ramosa ApaH (4) (PDB: 3Q9E) forming a salt bridge to Glu106 in the C-terminal end of L2-loop with the N1-amino group of the N8-acetylspermidine/N4-amino group of acetylspermine. This Glu106 in MrApaH is replaced by His106 in PsApaH (4) explaining the higher acetylpolyamine promiscuity. c The PEG-motif (yellow) in human HDAC10 (1g) is replaced by PIS (blue) in PsApaH (4). For HsHDAC10 (1g), the PEG-motif (273-PEG-275) contains the Glu gatekeeper creating selectivity for N8-acetylspermidine forming an electrostatic interaction with the secondary N4-amino group. This sequence is replaced by 290-PIS-292 in PsApaH (4) and other bacterial polyamine deacetylases. Shown is a superposition of the structure of PsApaH (4) and HsHDAC10 (1g) AF2. For CD1 of human HDAC6 (1g), HsHDAC6a, a Lys (green) is present at this position in the PKG-motif, which explains the preference to deacylate C-terminal Lys-side chains. d Electrostatic surface representation of PsApaH (4) and M. ramosa ApaH (4) in complex with acetylspermine (PDB: 3Q9E) shows sterically restricted access to the active site. The electrostatics were plotted onto the surface of the PsApaH (4) using the APBS plugin in PyMOL220.
