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Methionine-Rich Loop of Multicopper Oxidase McoA Follows Open-to-Close Transitions with a Role in Enzyme Catalysis

  • Patrícia T. Borges
    Patrícia T. Borges
    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
  • Vânia Brissos
    Vânia Brissos
    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
  • Guillem Hernandez
    Guillem Hernandez
    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
  • Laura Masgrau
    Laura Masgrau
    Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain
    Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
  • Maria Fátima Lucas
    Maria Fátima Lucas
    Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain
  • Emanuele Monza
    Emanuele Monza
    Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain
  • Carlos Frazão*
    Carlos Frazão
    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
    *Email: [email protected]
  • Tiago N. Cordeiro*
    Tiago N. Cordeiro
    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
    *Email: [email protected]
  • , and 
  • Lígia O. Martins*
    Lígia O. Martins
    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
    *Email: [email protected]
Cite this: ACS Catal. 2020, 10, 13, 7162–7176
Publication Date (Web):June 2, 2020
https://doi.org/10.1021/acscatal.0c01623
Copyright © 2020 American Chemical Society
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Abstract

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Multicopper oxidases oxidize a vast range of aromatic substrates coupled to the reduction of molecular oxygen to water. A vast broad spectrum of applications reflects their high biotechnological importance. The crystal structure of McoA from the hyperthermophilic bacteria Aquifex aeolicus has the most tightly compact and hydrophobic core among its prokaryotic counterparts. A 29-residue long loop enriched in glycines and methionines (Met-loop) close to the active T1 Cu center is not detected in the electron density maps. Accurate prediction of loop structures remains challenging, especially for long segments with sizable conformational space. Therefore, a combination of Rosetta and molecular dynamics simulations with ensemble-based small-angle X-ray scattering analysis was used to probe the conformational landscape of the Met-loop. The results indicate a highly flexible omega-loop, which is nevertheless not random but preferentially follows open-to-close transitions, exposing or occluding the T1 Cu site. Loop-truncated variants maintain wild-type stability and consistently lower and higher catalytic efficiencies (kcat/Km) for organic and metal substrates, respectively. Our results suggest that the loop transient dynamic equilibrium can exert important switch-like regulatory function, defining a role for Met-rich motifs as dynamic gate-gappers. This work provides insights into the dynamics of Met-rich loops essential to understand the molecular determinants of substrate promiscuity and catalytic rates within multicopper oxidases. We anticipate that engineering the Met-loop structural dynamics will unleash important changes in enzyme function and specificity with impact on their applications.

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The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acscatal.0c01623.

  • Procedures for the construction of McoA without signal peptide; solubility assays; UV–visible and CD spectra; benchmarking of Met-loop modeling; MD simulations; PCA analysis; primers information; protein production yields; kinetic parameters for ABTS and Cu(I) of wild-type and variant WT-loop5; long tunnel and short tunnel dimensions and polarity of prokaryotic MCOs; thermodynamic stability of McoA wild-type and WT-loop5; kinetic parameters of McoA wild-type and variants constrained in the Met-loop for ABTS and Cu(I); SDS-PAGE analysis of wild-type enzyme with and without signal peptide, UV–visible and CD spectra; structural comparison of A. aeolicus McoA and available prokaryotic MCOs structures; de novo reconstruction of McoC, McoP, and CueO loops; lowest scoring reconstructions selected based on Rosetta-energy and SAXS-based hybrid scoring for McoC, McoP, and CueO; evolution of χ2 as a function of Met-loop sub-ensemble size and Conformational ensemble representation of Met-loop; flexible Met-loop probed by SAXS; Met-loop MD simulations; and PCA and stability analysis on MCoA (PDF)

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