Enzymes in biosynthesis
Biosynthetic pathways towards natural products usually depend on highly specialized enzymes. This thematic issue calls for manuscripts covering various aspects of biosynthetic enzymes, including (but not limited to) functional characterization, enzyme mechanistic studies, structural work, and mutational investigations. Studies covering the application of enzymes in total synthesis or in the transformation of nonnatural substrate analogs are also welcome.
- Review
- Published 21 Jun 2022
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Figure 1: Examples of endoperoxide-containing natural products.
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Scheme 1: Reactions of COXs.
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Figure 2: Structures of COXs [52,53]. (A) The overall structure of ovine COX-1. (B and C) Comparison of the cyclooxy...
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Scheme 2: Proposed reaction mechanisms of COXs [24].
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Scheme 3: General reaction mechanism of Fe/2OG oxygenases.
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Scheme 4: Reaction of FtmOx1 [68-71].
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Figure 3: Structure of FtmOx1 [71]. (A) The FtmOx1 binary structure in complex with 2OG. (B and C) Comparison of ...
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Scheme 5: Proposed COX-like mechanism of FtmOx1 [68].
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Scheme 6: Proposed CarC-like mechanism of FtmOx1 [70].
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Scheme 7: Reaction of NvfI [28].
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Scheme 8: Possible reaction pathways leading to fumigatonoid A [28].
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Figure 4: Structure of NvfI [28]. (A–C) Conformational changes of loop regions: (A) open conformation, (B) partia...
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Scheme 9: Another possible reaction pathway for the formation of fumigatonoid A [28].
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- Full Research Paper
- Published 22 Jun 2022
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Figure 1: Prenylated aromatic metabolites are involved in cellular processes like cell respiration (coenzyme Q...
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Figure 2: Homology clustering of Ptases encoded in marine Flavobacteria and Saccharomonospora species (G1–G4,...
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Figure 3: Regional alignment of ubiA-297 of Maribacter sp. MS6 (EU359911.1) and homologous genes in Z. uligin...
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Figure 4: A) Amino acid alignment and binding residues of UbiA-297. G2-Ptases are illustrated in the grey box...
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Figure 5: Evaluation of substrate specificity of UbiA-297. Accepted substrates are shown in red, while no pro...
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Figure 6: A) Reaction scheme of UbiA-297 catalyzing the assumed para-directed farnesylation of 8-HQA; B) calc...
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- Letter
- Published 08 Jul 2022
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Scheme 1: Biosynthesis of 2-MIB (1). A) Naturally observed pathway through methylation of GPP to 2-Me-GPP by ...
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Figure 1: A) Active site of 2MIBS with the bound substrate surrogate 2FGPP (generated with Pymol from the cry...
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Scheme 2: Synthesis of (R)- and (S)-2-Me-LPP.
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Figure 2: Structures of 2MIBS side products and spontaneous degradation products of 2-Me-LPP. The enantiomers...
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Figure 3: Total ion chromatograms of extracts from an incubation of A) enantiomerically pure (R)-2-Me-LPP wit...
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Scheme 3: Hypothetical mechanism for the isomerization of (S)-2-Me-LPP through 2-Me-GPP to (R)-2-Me-LPP.
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- Full Research Paper
- Published 21 Jul 2022
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Figure 1: (a) The natural pathways (MVA: blue, MEP: green) for producing IPP and DMAPP; (b) the carbon skelet...
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Figure 2: Truncated artificial pathways (six steps) to produce terpentetriene and ent-kaurene.
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Figure 3: Construction maps of single plasmid expression system and two-plasmid expression system for overpro...
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Figure 4: Optimizing the ratios of ISO/DMAA for overproducing terpentetriene (a) and ent-kaurene (b). Red: IS...
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Figure 5: (a) Terpentetriene (red) and ent-kaurene (blue) yields supplied with various concentrations of glyc...
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- Full Research Paper
- Published 25 Jul 2022
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Figure 1: Chemical structures of compounds 1–8.
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Figure 2: ORTEP drawing of 2 (displacement ellipsoids are drawn at the 50% probability level).
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Figure 3: Experimental and calculated ECD curves of (+)-1.
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Figure 4: 1H-1H COSY, key HMBC correlations, and NOESY correlations of compound 5.
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Figure 5: Experimental ECD curves of compounds (+)-4, (−)-4 (top), (+)-5, and (−)-5 (bottom).
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Scheme 1: Proposed cyclization pathway of terpene intermediates and plausible post-modifications of compounds ...
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Figure 6: Compound 3 reduced the mRNA levels of TNF-α (left) and CCL2 (right) in LPS-stimulated RAW264.7 macr...
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- Full Research Paper
- Published 04 Aug 2022
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Figure 1: Summary of yields of HP and IE products in hydropyrene synthase.
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Scheme 1: Proposed mechanism for HP and IE routes.
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Figure 2: Free energy profile of hydropyrene cation (a), and IE cation (b) formation in the gas phase. The fr...
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Figure 3: Structures of intermediates C‘ and C. The distance between the double bond and the cation in interm...
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- Full Research Paper
- Published 09 Aug 2022
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Figure 1: Structures of compounds 1–6, atromentin, and echoside C.
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Figure 2: (A) Key 2D NMR correlations of compounds 1 and 2. (B) X-ray crystal structure of compounds 1 and 3.
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Figure 3: (A) The biosynthetic gene cluster of daturamycins. (B) Proposed biosynthetic pathway of daturamycin...
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Figure 4: (A) HPLC analysis of the fermentation extracts of mutant S. sp. KIB-H1544-∆datA. (B) SDS-PAGE analy...
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- Full Research Paper
- Published 10 Aug 2022
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Figure 1: Representative natural azoxides.
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Figure 2: Biosynthetic gene clusters of aliphatic azoxy natural products. Conserved proteins are colored acco...
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Scheme 1: N2H4-detecting colorimetric assay.
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Figure 3: Structures of azodyrecins (a) and new azodyrecin derivatives, azodyrecins D–G (7–10) (b). Key corre...
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Figure 4: In vitro characterization of Ady1. Extracted ion chromatograms at m/z 329.3 (black) and m/z 343.3 (...
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Scheme 2: Proposed biosynthetic pathway of azodyrecin.
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Figure 5: Sequence similarity network of VlmA-like enzymes in the actinobacterial genomes in the Refseq datab...
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- Full Research Paper
- Published 26 Aug 2022
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Figure 1: Structures of cattleyaisoflavones A (1), B (2), C (3), and daidzein (4).
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Figure 2: a) The culture in ISP-2 liquid did not produce 1–3, while feeding with 4 restored the production (a...
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Figure 3: CYP158C1 dimerizes 4 to form dimers 2 and 5 in vitro (analytical method B, 254 nm). Control conditi...
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Scheme 1: a) Compatible and b) incompatible substrates of CYP158C1. Products were identified using analytical...
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Scheme 2: Proposed mechanism of CYP158C1-mediated dimerization of isoflavones.
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- Full Research Paper
- Published 20 Sep 2022
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Figure 1: Polyphosphate, a ubiquitous phosphate storage molecule. Reported chain lengths range from three to ...
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Figure 2: Comparison of PPK1 and PPK2 enzymes. a) Reaction scheme; b) structure of the EcPPK1 monomer (PDB 1X...
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Figure 3: a) Kinases as ATP regeneration enzymes, exemplified by the hexokinase-catalysed ATP-dependent phosp...
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Figure 4: Time courses of reactions started with ADP catalysed by a) SmPPK2 and b) EcPPK1. Time courses of re...
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Figure 5: a) Ratio of product to substrate for the three nucleotide concentrations (0.5, 2, and 4 mM) used in...
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Figure 6: Time courses comparing EcPPK1 (blue) and SmPPK2 (green) for ATP synthesis (a) and ATP degradation (...
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- Review
- Published 21 Sep 2022
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Figure 1: Enzyme function of cytochrome P450 monooxygenases (CYPs). A) Typical net reaction of CYPs, resultin...
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Figure 2: Phylogenetic distribution of CYPs acting on triterpenoid and steroid scaffolds (red nodes) compared...
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Figure 3: CYPs modifying steroid (A), cucurbitacin steroid (B) and tetracyclic triterpene (C) backbones. Subs...
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Figure 4: CYPs modifying pentacyclic 6-6-6-6-6 triterpenes. Substructures in grey indicate regions where majo...
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Figure 5: CYPs modifying pentacyclic 6-6-6-6-5 triterpenes (A) and unusual triterpenes (B). Substructures in ...
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Figure 6: Recent examples of multifunctional CYPs in triterpenoid and steroid metabolism in plants that insta...
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- Full Research Paper
- Published 05 Oct 2022
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Figure 1: The five distinct FC-type DTSs and the corresponding products.
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Figure 2: Bioinformatics analysis of the tad cluster. A) Phylogenetic tree of TadA and representative fungal ...
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Figure 3: HPLC–MS analysis of mycelial extracts from A. oryzae NSAR1 transformants. A) The HPLC profiles moni...
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Scheme 1: Biosynthesis of FC-type diterpenoids. A) The biosynthetic pathway of 1, 2 and 4. B) Cyclization mec...
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- Perspective
- Published 06 Dec 2022
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Figure 1: Examples of prominent natural products: N-butyrylhomoserine lactone (1), pyoverdin (2), malleicypro...
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Figure 2: Biosynthetic principles of (A) assembly line-like pathways and (B) discrete multi-enzymatic assembl...
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Figure 3: Universal (A, B, F) NP class and NP family-specific (C, D, F) signature sequences in NP BGCs and se...
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Figure 4: Concepts of algorithms in order of complexity and examples of genome mining tools that employ the r...
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Figure 5: Examples of peptide NPs, the corresponding BGCs of which were determined through retrobiosynthetic ...
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Figure 6: gcBGC prioritization process. The bar represents all identified gene clusters in one organism and i...
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Figure 7: Genome alignments of related organisms revealing the presence of syntenic (purple) as well as non-s...
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