8DK0

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

Summary for 8DK0

• Entry DOI: 10.2210/pdb8dk0/pdb
• Related: 7RIS 7RIZ 8DIZ 8DJF
• Descriptor: Gluconolactonase, CALCIUM ION, SODIUM ION, ... (5 entities in total)
• Functional Keywords: gamma-valerolactone, hydrolase
• Biological source: Rhodopseudomonas palustris CGA009
• Total number of polymer chains: 1
• Total formula weight: 33289.92

Authors

Bingman, C.A.,Hall, B.W.,Smith, R.W.,Fox, B.G.,Donohue, T.J. (deposition date: 2022-07-01, release date: 2023-01-11, Last modification date: 2023-10-25)

Primary citation

Hall, B.W.,Bingman, C.A.,Fox, B.G.,Noguera, D.R.,Donohue, T.J.
A broad specificity beta-propeller enzyme from Rhodopseudomonas palustris that hydrolyzes many lactones including gamma-valerolactone.
J.Biol.Chem., 299:102782-102782, 2022

PubMed Abstract: Lactones are prevalent in biological and industrial settings, yet there is a lack of information regarding enzymes used to metabolize these compounds. One compound, γ-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-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 β-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 WT 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 β-propeller lactonases suggests this mechanism may be relevant for other members of this emerging class of versatile catalysts.

PubMed: 36502920
DOI: 10.1016/j.jbc.2022.102782

Experimental method

X-RAY DIFFRACTION (1.55 Å)