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Advances in Biocatalysis and Enzyme Engineering

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

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 14974

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Special Issue Editors

Dr. Jing Zhao

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Guest Editor

State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, #368 Youyi Road, Wuhan 430062, China
Interests: enzyme engineering; biocatalysis; computational biology; multienzyme cascade reaction
Special Issues, Collections and Topics in MDPI journals

Dr. Guochao Xu

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Guest Editor

School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, China
Interests: enzyme engineering; directed evolution; cell-free biosynthesis; cofactor engineering

Special Issue Information

Dear Colleagues,

Biocatalysis using enzymes or whole cells has become an essential tool in the synthesis of chemicals. As an alternative to traditional chemical processes, biocatalysis is particularly attractive in synthesizing chiral compounds and performing chemically challenging reactions. The discovery and characterization of novel enzymes is important to broaden the applicability of biocatalysis, and engineering of existing enzymes using genetic or chemical modifications not only can deepen our understanding of enzyme structure-function relationship but can also improve biocatalysis with better catalytic performance. In recent years, multienzymatic/cell-free biosynthetic and chemoenzymatic cascade reactions have attracted more attention because they can significantly expand the product scope and synthesize more complex target molecules.

This Special Issue aims to collect original research articles and reviews focused on biocatalysis and enzyme engineering. Submissions from biocatalytic reactions coupled with other types of catalysis such as chemocatalysis or photocatalysis are also welcome.

Dr. Jing Zhao

Dr. Guochao Xu

Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Catalysts is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

enzyme
biocatalysis
enzyme discovery
enzyme engineering
directed evolution
rational design
enzyme mechanism
machine learning
multienzymatic synthesis/cell-free biosynthesis
chemoenzymatic synthesis
artificial cofactor

Published Papers (7 papers)

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Research

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18 pages, 2162 KiB

Open AccessArticle

Discovery and Heterologous Expression of Unspecific Peroxygenases

by Katharina Ebner, Lukas J. Pfeifenberger, Claudia Rinnofner, Veronika Schusterbauer, Anton Glieder and Margit Winkler

Catalysts 2023, 13(1), 206; https://doi.org/10.3390/catal13010206 - 16 Jan 2023

Cited by 14 | Viewed by 3589

Abstract

Since 2004, unspecific peroxygenases, in short UPOs (EC. 1.11.2.1), have been explored. UPOs are closing a gap between P450 monooxygenases and chloroperoxidases. These enzymes are highly active biocatalysts for the selective oxyfunctionalisation of C–H, C=C and C-C bonds. UPOs are secreted fungal proteins and Komagataella phaffii (Pichia pastoris) is an ideal host for high throughput screening approaches and UPO production. Heterologous overexpression of 26 new UPOs by K. phaffii was performed in deep well plate cultivation and shake flask cultivation up to 50 mL volume. Enzymes were screened using colorimetric assays with 2,2-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), 2,6-dimethoxyphenol (DMP), naphthalene and 5-nitro-1,3-benzodioxole (NBD) as reporter substrates. The PaDa-I (AaeUPO mutant) and HspUPO were used as benchmarks to find interesting new enzymes with complementary activity profiles as well as good producing strains. Herein we show that six UPOs from Psathyrella aberdarensis, Coprinopsis marcescibilis, Aspergillus novoparasiticus, Dendrothele bispora and Aspergillus brasiliensis are particularly active. Full article

(This article belongs to the Special Issue Advances in Biocatalysis and Enzyme Engineering)

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11 pages, 6659 KiB

Open AccessArticle

A Combined Computational–Experimental Study on the Substrate Binding and Reaction Mechanism of Salicylic Acid Decarboxylase

by Fuqiang Chen, Yipei Zhao, Chenghua Zhang, Wei Wang, Jian Gao, Qian Li, Huimin Qin, Yujie Dai, Weidong Liu, Fufeng Liu, Hao Su and Xiang Sheng

Catalysts 2022, 12(12), 1577; https://doi.org/10.3390/catal12121577 - 4 Dec 2022

Viewed by 1912

Abstract

Salicylic acid decarboxylase (SDC) from the amidohydrolase superfamily (AHS) catalyzes the reversible decarboxylation of salicylic acid to form phenol. In this study, the substrate binding mode and reaction mechanism of SDC were investigated using computational and crystallographic methods. Quantum chemical calculations show that the enzyme follows the general mechanism of AHS decarboxylases. Namely, the reaction begins with proton transfer from a metal-coordinated aspartic acid residue (Asp298 in SDC) to the C1 of salicylic acid, which is followed by the C–C bond cleavage, to generate the phenol product and release CO₂. Interestingly, the calculations show that SDC is a Mg-dependent enzyme rather than the previously proposed Zn-dependent, and the substrate is shown to be bidentately coordinated to the metal center in the catalysis, which is also different from the previous proposal. These predictions are corroborated by the crystal structure of SDC solved in complex with the substrate analogue 2-nitrophenol. The mechanistic insights into SDC in the present study provide important information for the rational design of the enzyme. Full article

(This article belongs to the Special Issue Advances in Biocatalysis and Enzyme Engineering)

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13 pages, 1839 KiB

Open AccessFeature PaperArticle

Not a Mistake but a Feature: Promiscuous Activity of Enzymes Meeting Mycotoxins

by Ilya Lyagin, Nikolay Stepanov, Olga Maslova, Olga Senko, Aysel Aslanli and Elena Efremenko

Catalysts 2022, 12(10), 1095; https://doi.org/10.3390/catal12101095 - 22 Sep 2022

Cited by 6 | Viewed by 1434

Abstract

Mycotoxins are dangerous compounds and find multiple routes to enter living bodies of humans and animals. To solve the issue and degrade the toxicants, (bio)catalytic processes look very promising. Hexahistidine-tagged organophosphorus hydrolase (His₆-OPH) is a well-studied catalyst for degradation of organophosphorus neurotoxins and lactone-containing quorum-sensing signal molecules. Moreover, the catalytic characteristics in hydrolysis of several mycotoxins (patulin, deoxynivalenol, zearalenone, and sterigmatocystin) were studied in this investigation. The best Michaelis constant and catalytic constant were estimated in the case of sterigmatocystin and patulin, respectively. A possible combination of His₆-OPH with inorganic sorbents treated by low-temperature plasma was investigated. Further, enzyme–polyelectrolyte complexes of poly(glutamic acid) with His₆-OPH and another enzymatic mycotoxin degrader (thermolysin) were successfully used to modify fiber materials. These catalytically active prototypes of protective materials appear to be useful for preventing surface contact and exposure to mycotoxins and other chemicals that are substrates for the enzymes used. Full article

(This article belongs to the Special Issue Advances in Biocatalysis and Enzyme Engineering)

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14 pages, 3860 KiB

Open AccessArticle

Origin of the Unexpected Enantioselectivity in the Enzymatic Reductions of 5-Membered-Ring Heterocyclic Ketones Catalyzed by Candida parapsilosis Carbonyl Reductases

by Byu Ri Sim, Jie Gu, Yvette Ley, Shenggan Luo, Yihan Liu, Qin Chen, Yao Nie and Yi-Lei Zhao

Catalysts 2022, 12(10), 1086; https://doi.org/10.3390/catal12101086 - 21 Sep 2022

Cited by 4 | Viewed by 1644

Abstract

Candida parapsilosis carbonyl reductases (CpRCR) have been widely used for the reductive conversion of ketone precursors and chiral alcohol products in pharmaceutical industries. The enzymatic enantioselectivity is believed to be related to the shape complementation between the cavities in the enzymes and the substitutions of the ketone substrates. In this work, we reported an unexpected enantioselectivity in the enzyme reductions of dihydrofuran-3(2H)-one (DHF) to (S)-tetrahydrofuran-3-ol (DHF-ol, enantiomeric excess: 96.4%), while dihydrothiophen-3(2H)-one substrate (DHT) was unproductive under the same experimental conditions. To rationalize the exclusive S-configuration and the specific reactivity of DHF, we carried out molecular dynamics simulations for the reacting complexations of DHF with CpRCR, and DHT with CpRCR. Our calculations indicate that DHF preferentially binds to the small cavity near L119, F285, and W286, while the large cavity near the α1 helix was mainly occupied by solvent water molecules. Moreover, the pre-reaction state analysis suggests that the pro-S conformations were more abundant than the pro-R, in particular for DHF. This suggests that the non-polar interaction of substrate C4-C5 methylene contacting the hydrophobic side-chains of L119-F285-W286, and the polar interaction of funanyl oxygen exposing the solvent environment play important roles in the enantioselectivity and reactivity. The phylogenetic tree of CpRCR homologues implies that a variety of amino acid combinations at positions 285 and 286 were available and thereby potentially useful for redesigning enantioselective reductions of 5-membered-ring heterocyclic ketones. Full article

(This article belongs to the Special Issue Advances in Biocatalysis and Enzyme Engineering)

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11 pages, 2156 KiB

Open AccessArticle

Protein Engineering of Pasteurella multocida α2,3-Sialyltransferase with Reduced α2,3-Sialidase Activity and Application in Synthesis of 3′-Sialyllactose

by Rui Yang, Mengge Gong, Siming Jiao, Juntian Han, Cui Feng, Meishan Pei, Zhongkai Zhou, Yuguang Du and Jianjun Li

Catalysts 2022, 12(6), 579; https://doi.org/10.3390/catal12060579 - 25 May 2022

Cited by 2 | Viewed by 1780

Abstract

Sialyltransferases are key enzymes for the production of sialosides. The versatility of Pasteurella multocida α2,3-sialyltransferase 1 (PmST1) causes difficulties in the efficient synthesis of α2,3-linked sialylatetd compounds, especial its α2,3-sialidase activity. In the current study, the α2,3-sialidase activity of PmST1 was further reduced by rational design-based protein engineering. Three double mutants PMG1 (M144D/R313Y), PMG2 (M144D/R313H) and PMG3 (M144D/R313N) were designed and constructed using M144D as the template and kinetically investigated. In comparison with M144D, the α2,3-sialyltransferase activity of PMG2 was enhanced by 1.4-fold, while its α2,3-sialidase activity was reduced by 4-fold. Two PMG2-based triple mutants PMG2-1 (M144D/R313H/T265S) and PMG2-2 (M144D/R313H/E271F) were then designed, generated and characterized. Compared with PMG2, triple mutants showed slightly improved α2,3-sialyltransferase activity, but their α2,3-sialidase activities were increased by 2.1–2.9 fold. In summary, PMG2 was used for preparative-scale production of 3′-SL (3′-sialyllactose) with a yield of >95%. These new PmST1 mutants could be potentially utilized for efficient synthesis of α2,3-linked sialosides. This work provides a guide to designing and constructing efficient sialyltransferases. Full article

(This article belongs to the Special Issue Advances in Biocatalysis and Enzyme Engineering)

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18 pages, 3309 KiB

Open AccessArticle

Synthesis of (S)- and (R)-β-Tyrosine by Redesigned Phenylalanine Aminomutase

by Fei Peng, Habibu Aliyu, André Delavault, Ulrike Engel and Jens Rudat

Catalysts 2022, 12(4), 397; https://doi.org/10.3390/catal12040397 - 1 Apr 2022

Viewed by 1986

Abstract

Phenylalanine aminomutase from Taxus chinensis (TchPAM) is employed in the biosynthesis of the widely used antitumor drug paclitaxel. TchPAM has received substantial attention due to its strict enantioselectivity towards (R)-β-phenylalanine, in contrast to the bacterial enzymes classified as EC 5.4.3.11 which are (S)-selective for this substrate. However, the understanding of the isomerization mechanism of the reorientation and rearrangement reactions in TchPAM might support and promote further research on expanding the scope of the substrate and thus the establishment of large-scale production of potential synthesis for drug development. Upon conservation analysis, computational simulation, and mutagenesis experiments, we report a mutant from TchPAM, which can catalyze the amination reaction of trans-p-hydroxycinnamic acid to (R)- and (S)-β-tyrosine. We propose a mechanism for the function of the highly conserved residues L179, N458, and Q459 in the active site of TchPAM. This work highlights the importance of the hydrophobic residues in the active site, including the residues L104, L108, and I431, for maintaining the strict enantioselectivity of TchPAM, and the importance of these residues for substrate specificity and activation by altering the substrate binding position or varying the location of neighboring residues. Furthermore, an explanation of (R)-selectivity in TchPAM is proposed based on the mutagenesis study of these hydrophobic residues. In summary, these studies support the future exploitation of the rational engineering of corresponding enzymes with MIO moiety (3,5-dihydro-5-methylidene-4H-imidazole-4-one) such as ammonia lyases and aminomutases of aromatic amino acids. Full article

(This article belongs to the Special Issue Advances in Biocatalysis and Enzyme Engineering)

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Review

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20 pages, 9329 KiB

Open AccessEditor’s ChoiceReview

Application of Laccase Catalysis in Bond Formation and Breakage: A Review

by Huan Lin, Zongjiang Yu, Qian Wang, Yaojie Liu, Long Jiang, Chao Xu and Mo Xian

Catalysts 2023, 13(4), 750; https://doi.org/10.3390/catal13040750 - 14 Apr 2023

Cited by 7 | Viewed by 1732

Abstract

Laccase belongs to the superfamily of multicopper oxidases and has been widely investigated in recent decades. Due to its mild and efficient oxidation of substrates, laccase has been successfully applied in organic catalytic synthesis, the degradation of harmful substances, and other green catalytic fields. Nevertheless, there are few reports on the green catalysis with laccase. This review focuses on reporting and collating some of the latest interesting laccase-catalyzed bond formation and breakage research. This is discussed with a focus on the effects of the medium system on the laccase-catalyzed reaction, as well as the formation and the breakage of C–N, C–C, and C–O bonds catalyzed by laccase. It provides abundant references and novel insights for furthering the industrial applications of laccase. Full article

(This article belongs to the Special Issue Advances in Biocatalysis and Enzyme Engineering)

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