Crystal structure of RPA3624, a beta-propeller lactonase from Rhodopseudomonas palustris, with active-site bound phosphate

Experimental Data Snapshot

  • Resolution: 1.72 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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This is version 1.2 of the entry. See complete history


A broad specificity beta-propeller enzyme from Rhodopseudomonas palustris that hydrolyzes many lactones including gamma-valerolactone.

Hall, B.W.Bingman, C.A.Fox, B.G.Noguera, D.R.Donohue, T.J.

(2022) J Biol Chem 299: 102782-102782

  • DOI: https://doi.org/10.1016/j.jbc.2022.102782
  • Primary Citation of Related Structures:  
    7RIS, 7RIZ, 8DJF, 8DJZ, 8DK0

  • 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 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 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.

  • Organizational Affiliation

    Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA; Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-propeller lactonase309Rhodopseudomonas palustris CGA009Mutation(s): 0 
Gene Names: RPA3624
Find proteins for Q6N3R9 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore Q6N3R9 
Go to UniProtKB:  Q6N3R9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6N3R9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.54α = 90
b = 44.54β = 90
c = 189.95γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0018409

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-01-18
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection