Fig. 5: Bacterial sub-cluster 1b enzymes are robust deacetylases forming tetramers in solution.
From: Distribution and diversity of classical deacylases in bacteria
a Bacterial sub-cluster 1b enzymes form tetramers in solution mediated by the N-terminal L1-loop and by an additional α-helix in an extended loop leading to the C-terminal α-helix (Gln-rich helix Q-rH in KpHdaH (1b)). Left panel: The tetramers consist of two head-to-head dimers arranged side-by-side. The L1-loop of each monomer subunit (M1-M4) contacts all remaining subunits of the tetramer and of the substrate. The L2-loop encompasses a β-hairpin motif placed in the interface of the tetramer. Right panel: Analyses of the interface area and mutational studies suggest two head-to-head dimers form the tetramer by side-to-side arrangement. b Closeup of the tetramer interface area reveals interactions needed for the composition of the integral tetramer. As an example, head-to-head dimer formation is mediated by the main-chain carbonyl of Cys208/Cys207 of one subunit (monomer: M) forming hydrogen bonds to the side chains of Gln347/Trp346 of the other subunit of KpHdaH (1b), respectively. Moreover, Gln32 of the L1-loop of one monomer forms a direct interaction with Asn51 of the other monomer. c The active site is almost perpendicular to the foot pocket. The architecture of the foot pocket needed for substrate release explains the preference of KpHdaH (1b) to act as a robust deacetylase. d The foot pocket is extended in VcHdaH (5b) compared to KpHdaH (1b) allowing it to accommodate the decanoic acid. The RPP-motif is replaced in VcHdaH (5b) by 132-SGGYHH-137 and the XGGY-motif by 290-GGGY-294 explaining structurally how the foot pocket in VcHdaH (5b) is able to accommodate the longer acyl-chain. The RP-peptide bond in the RPP-motif is in cis-configuration resulting in restricting the volume of the foot pocket. Tyr1355b (superscript 5b: VcHdaH (5b); superscript 1b: KpHdaH (1b)) lines the alkyl chain of the fatty acid (induced fit mechanism) and the extended Gly-rich GGGY-motif in VcHdaH (5b) allows structural flexibility for the active site Tyr2945b. e Multiple sequence alignment of the RPP- and XGGY-motif lining the foot pocket. All robust deacetylases show a conserved RPP- and XGGY-motif as shown for bacterial deacetylases and selected classical HDACs.
