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Enzymes, Pathways and Intermediates of Bacterial Metabolism

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 3877

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Special Issue Editor

Prof. Dr. Alessio Peracchi

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Guest Editor

Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
Interests: enzymes; enzyme evolution; kinetics; metabolism; functional proteomics

Special Issue Information

Dear Colleagues,

Bacteria are biochemically very rich and diverse, possessing myriads of pathways (often very specialized) that are a treasure trove of new enzymes and new chemistries. In recent years, the exponentially increasing number of sequenced bacterial genomes and metagenomes has offered opportunities to identify new enzymes and explore metabolic pathways. The task is facilitated by the fact that the genes encoding enzymes involved in a particular pathway very often co-localize in the genome, forming operons and gene clusters. Additionally, the availability of genetic tools for the knockout of specific genes represents a valuable tool for the validation of functions. In turn, these studies add to our knowledge of microbial biochemistry, especially (but not solely) of secondary metabolism. This knowledge unveils, for example, new targets for antimicrobial therapy and new catalysts for applicative purposes. Further, these studies have implications for environmental microbiology and for understanding the impact of microbiota in human health.

Prof. Dr. Alessio Peracchi
Guest Editor

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Keywords

bacterial enzymes
metabolic pathways
secondary metabolism
microbial biodegradation
functional genomics
bacterial enzyme mechanism

Published Papers (2 papers)

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Research

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17 pages, 4016 KiB

Open AccessArticle

Structural Determinants of the Specific Activities of an L-Amino Acid Oxidase from Pseudoalteromonas luteoviolacea CPMOR-1 with Broad Substrate Specificity

by Kyle J. Mamounis, Maria Luiza Caldas Nogueira, Daniela Priscila Marchi Salvador, Andres Andreo-Vidal, Antonio Sanchez-Amat and Victor L. Davidson

Molecules 2022, 27(15), 4726; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27154726 - 24 Jul 2022

Cited by 3 | Viewed by 1511

Abstract

The Pseudoalteromonas luteoviolacea strain CPMOR-1 expresses a flavin adenine dinucleotide (FAD)-dependent L-amino acid oxidase (LAAO) with broad substrate specificity. Steady-state kinetic analysis of its reactivity towards the 20 proteinogenic amino acids showed some activity to all except proline. The relative specific activity for amino acid substrates was not correlated only with K_m or k_cat values, since the two parameters often varied independently of each other. Variation in K_m was attributed to the differential binding affinity. Variation in k_cat was attributed to differential positioning of the bound substrate relative to FAD that decreased the reaction rate. A structural model of this LAAO was compared with structures of other FAD-dependent LAAOs that have different substrate specificities: an LAAO from snake venom that prefers aromatic amino acid substrates and a fungal LAAO that is specific for lysine. While the amino acid sequences of these LAAOs are not very similar, their overall structures are comparable. The differential activity towards specific amino acids was correlated with specific residues in the active sites of these LAAOs. Residues in the active site that interact with the amino and carboxyl groups attached to the α-carbon of the substrate amino acid are conserved in all of the LAAOs. Residues that interact with the side chains of the amino acid substrates show variation. This provides insight into the structural determinants of the LAAOs that dictate their different substrate preferences. These results are of interest for harnessing these enzymes for possible applications in biotechnology, such as deracemization. Full article

(This article belongs to the Special Issue Enzymes, Pathways and Intermediates of Bacterial Metabolism)

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Review

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22 pages, 4696 KiB

Open AccessReview

Biosynthesis of DNA-Alkylating Antitumor Natural Products

by Qiu-Yue Nie, Yu Hu, Xian-Feng Hou and Gong-Li Tang

Molecules 2022, 27(19), 6387; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27196387 - 27 Sep 2022

Cited by 3 | Viewed by 1826

Abstract

DNA-alkylating natural products play an important role in drug development due to their significant antitumor activities. They usually show high affinity with DNA through different mechanisms with the aid of their unique scaffold and highly active functional groups. Therefore, the biosynthesis of these natural products has been extensively studied, especially the construction of their pharmacophores. Meanwhile, their producing strains have evolved corresponding self-resistance strategies to protect themselves. To further promote the functional characterization of their biosynthetic pathways and lay the foundation for the discovery and rational design of DNA alkylating agents, we summarize herein the progress of research into DNA-alkylating antitumor natural products, including their biosynthesis, modes of action, and auto-resistance mechanisms. Full article

(This article belongs to the Special Issue Enzymes, Pathways and Intermediates of Bacterial Metabolism)

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