The Design of Protein-Based Catalysts

A special issue of Catalysts (ISSN 2073-4344). This special issue belongs to the section "Biocatalysis".

Deadline for manuscript submissions: 31 March 2025 | Viewed by 987

Special Issue Editor


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Guest Editor
3B’s Research Group, Universidade do Minho, Braga, Portugal
Interests: catalysis; enzyme modification; biocatalysis; synthesis; biomaterial design
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Special Issue Information

Dear Colleagues,

The present Special Issue aims to combine a group of articles devoted to the use of protein-based catalysts. Biocatalysis is unquestionably one of the major pillars of sustainable and green chemistry. Protein-based catalysts have numerous applications outside of biological systems. They are widely used in industry, medicine, and biotechnology. Additionally, scientists are actively researching and engineering new enzymes with enhanced catalytic properties for specific applications.

Articles devoted to all applications of proteins-based catalysts in the most distinguished fields in the form of original research papers, review articles, and short communications are welcome.

If you would like to submit papers to this Special Issue or have any questions, please contact the in-house editor, Dr. Duangkamon Phuakkhaw ([email protected]).

Dr. Jennifer Noro
Guest Editor

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Keywords

  • proteins
  • enzymes
  • biocatalysis
  • protein modification
  • sustainable and green synthesis

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Published Papers (1 paper)

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Research

19 pages, 3991 KiB  
Article
Diverse YqeK Diadenosine Tetraphosphate Hydrolases Control Biofilm Formation in an Iron-Dependent Manner
by Chie Ueda, Natalie Chin, Qianyi Yang, Luying Pan, Rheann Ponniah and Maria-Eirini Pandelia
Catalysts 2024, 14(9), 652; https://doi.org/10.3390/catal14090652 - 23 Sep 2024
Viewed by 680
Abstract
YqeK is a bacterial HD-domain metalloprotein that hydrolyzes the putative second messenger diadenosine tetraphosphate (Ap4A). Elevated Ap4A levels are primarily observed upon exposure of bacteria to factors such as heat or oxidative stress and cause pleiotropic effects, including antibiotic sensitivity and disrupted biofilm [...] Read more.
YqeK is a bacterial HD-domain metalloprotein that hydrolyzes the putative second messenger diadenosine tetraphosphate (Ap4A). Elevated Ap4A levels are primarily observed upon exposure of bacteria to factors such as heat or oxidative stress and cause pleiotropic effects, including antibiotic sensitivity and disrupted biofilm formation. Ap4A thus plays a central role in bacterial physiology and metabolism, and its hydrolysis by YqeK is intimately linked to the ability of these microbes to cope with stress. Although YqeK is reported to hydrolyze Ap4A under aerobic conditions, all four existing crystal structures reveal an active site that consists of a diiron center, portraying a cryptic chemical nature for the active metallocofactor. This study examines two YqeK proteins from two ecologically diverse parent organisms: the obligate anaerobe Clostridium acetobutylicum and the facultative aerobe Bacillus halodurans. Both enzymes utilize Fe-based cofactors for catalysis, while under ambient or oxidative conditions, Bh YqeK hydrolyzes Ap4A more efficiently compared to Ca YqeK. This redox-dependent activity difference stems from the following two molecular mechanisms: the incorporation of mixed-metal, Fe-based bimetallic cofactors, in which the second metal is redox inert (i.e., Fe–Zn) and the upshift of the Fe–Fe cofactor reduction potentials. In addition, three strictly conserved, positively charged residues vicinal to the active site are critical for tuning Ap4A hydrolysis. In conclusion, YqeK is an Fe-dependent phosphohydrolase that appears to have evolved to permit Ap4A hydrolysis under different environmental niches (aerobic vs. anaerobic) by expanding its cofactor configuration and O2 tolerance. Full article
(This article belongs to the Special Issue The Design of Protein-Based Catalysts)
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