Structure and Dynamics of an Archeal Monoglyceride Lipase from Palaeococcus ferrophilus as Revealed by Crystallography and In Silico Analysis

Abstract

The crystallographic analysis of a lipase from Palaeococcus ferrophilus (PFL) previously annotated as a lysophospholipase revealed high structural conservation with other monoglyceride lipases, in particular in the lid domain and substrate binding pockets. In agreement with this observation, PFL was shown to be active on various monoacylglycerols. Molecular Dynamics (MD) studies performed in the absence and in the presence of ligands further allowed characterization of the dynamics of this system and led to a systematic closure of the lid compared to the crystal structure. However, the presence of ligands in the acyl-binding pocket stabilizes intermediate conformations compared to the crystal and totally closed structures. Several lid-stabilizing or closure elements were highlighted, i.e., hydrogen bonds between Ser117 and Ile204 or Asn142 and its facing amino acid lid residues, as well as Phe123. Thus, based on this complementary crystallographic and MD approach, we suggest that the crystal structure reported herein represents an open conformation, at least partially, of the PFL, which is likely stabilized by the ligand, and it brings to light several key structural features prone to participate in the closure of the lid.

Structural Changes in the Cap of Rv0183/mtbMGL Modulate the Shape of the Binding Pocket

“…To fully understand the activity of mtbMGL, it is still necessary to confirm the proposed substrate interactions [ 18 ] experimentally and to study conformational changes of the cap, both of which are addressed in this work. Similar cap domains are also found in MGLs from other organisms (human [ 19 ], yeast [ 20 ], bacteria [ 21 ], archaea [ 22 ]) and are thought to be a distinctive feature [ 23 ]. For hMGL, extensive research was performed on the connection between activity and structural changes in the cap domain.…”

“…Despite the low sequence homology of MGLs, they share the common α/β-hydrolase core fold and the conserved cap architecture [ 23 ]. Extensive research was performed on the relationship between conformational changes in the cap domain of hMGLs, and their activities in relation to open and closed states [ 19 , 22 , 24 , 25 , 42 ]. Combined with the changes presented herein in the cap domain of mtbMGL, new questions arise.…”

“…Additionally, any structure-based drug development effort will benefit from including data on conformational changes in the binding pocket. The different conformations in the cap region of experimentally derived crystal structures of MGLs from different organisms [ 18 , 19 , 20 , 21 , 22 , 43 , 44 ], elegant NMR, and hydrogen–deuterium exchange mass spectrometry studies on human MGL [ 24 , 25 ] or molecular dynamics approaches [ 22 ] should be taken into account in structure-guided approaches for compound screening [ 45 ]. These benefits can be envisaged for in silico docking approaches for repurposing drugs or in the design of novel, specifically binding inhibitors of proteins from numerous pathogenic organisms [ 46 ].…”

Global atlas of predicted functional domains inLegionella pneumophilaDot/Icm translocated effectors

“…The remaining 8 putative ɑ/β hydrolases show very low sequence identity with structurally and functionally characterized proteins. Some of the predicted features that may provide a cue to the function of these effectors include a long, deep, hydrophobic cleft in the model of Lpg1642 that is reminiscent of the ligand binding site in the monoacylglycerol lipase from Palaeococcus ferrophilus (PDB 6QE2) (Labar et al , 2021), and the model of Lpg2391 shows a broad, wide, and deep cleft.…”