8dk0

Crystal structure of RPA3624, a beta-propeller lactonase from Rhodopseudomonas palustris, with active-site bound (S)gamma-valerolactone

spinqualitylabelsall models 8dk0, resolution 1.55Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 8dk0 is a 1 chain structure with sequence from Rhodopseudomonas palustris CGA009. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.55Å Ligands: CA, NA, YVR Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q6N3R9_RHOPA Publication Abstract from PubMed Lactones are prevalent in biological and industrial settings, yet there is a lack of information regarding enzymes used to metabolize these compounds. One compound, gamma-valerolactone (GVL), is used as a solvent to dissolve plant cell walls into sugars and aromatic molecules for subsequent microbial conversion to fuels and chemicals. Despite the promise of GVL as a renewable solvent for biomass deconstruction, residual GVL can be toxic to microbial fermentation. Here, we identified a Ca(2+)-dependent enzyme from Rhodopseudomonas palustris (Rpa3624) and showed that it can hydrolyze aliphatic and aromatic lactones and esters, including GVL. Maximum-likelihood phylogenetic analysis of other related lactonases with experimentally determined substrate preferences shows that Rpa3624 separates by sequence motifs into a subclade with preference for hydrophobic substrates. Additionally, we solved crystal structures of this beta-propeller enzyme separately with either phosphate, an inhibitor, or a mixture of GVL and products to define an active site where calcium-bound water and calcium-bound aspartic and glutamic acid residues make close contact with substrate and product. Our kinetic characterization of wild type and mutant enzymes combined with structural insights inform a reaction mechanism that centers around activation of a calcium-bound water molecule promoted by general base catalysis and close contacts with substrate and a potential intermediate. Similarity of Rpa3624 with other beta-propeller lactonases suggests this mechanism may be relevant for other members of this emerging class of versatile catalysts. A broad specificity beta-propeller enzyme from Rhodopseudomonas palustris that hydrolyzes many lactones including gamma-valerolactone.,Hall BW, Bingman CA, Fox BG, Noguera DR, Donohue TJ J Biol Chem. 2022 Dec 8:102782. doi: 10.1016/j.jbc.2022.102782. PMID:36502920 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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