Structural insights into CYP107G1 from rapamycin-producing Streptomyces rapamycinicus

Kim, Vitchan; Lim, Young-Ran; Lee, Inho; Lee, Jong-Ha; Han, S.H.; Pham, Tan‐Viet; Kim, Harim; Lee, Rowoon; Kang, Lin‐Woo; Kim, Donghak

doi:10.1016/j.abb.2020.108544

Cited by 7 publications

(8 citation statements)

References 28 publications

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“…The genes encoding CYP107 (detected in this study) are among those reported to belong to biosynthetic gene clusters (BGCs) of Bacillus species constituting 61% (n = 68) of those reported in the database (Mthethwa et al 2018). CYP107 have been found to be more highly conserved in Bacillus and Streptomyces (Mnguni et al 2020), and many are involved in the synthesis of macrolide antibiotics (Kim et al 2020). One of the subfamilies of this group annotated in this study CYP107DY1 is a recently discovered plasmid encoded protein in Bacillus megaterium, which acts on mevastatin to produce pravastatin, a drug used in the treatment of hypercholesterolemia (Milhim et al 2016).…”

Section: Discussionmentioning

confidence: 68%

Deciphering the cytochrome P450 genes in the microbiome of a chronically polluted soil with history of agricultural activities

et al. 2022

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Background Cytochrome P450 monooxygenases (CYPs) are exciting biocatalysts that catalyzes diverse regio- and stereoselective reactions of a broad range of substrates. The cytochrome P450 genes (CYPomes) of a chronically polluted soil (3S) with history of agricultural activities were deciphered via functional annotation of putative ORFs (open reading frames) using KEGG KofamKOALA, PHMMER, the Cytochrome P450 Engineering Database CYPED v6.0, and the NCBI Batch Web CD-Search tool. Results Annotation revealed the detection of seventy-seven CYP families and eight standalone CYPs cutting across the three domains of life. The prokaryote CYPome has 72 CYP families, 93 subfamilies, and seven standalone CYPs. The phylum Proteobacteria and the genera Streptomyces, Mycobacterium, and Bacillus with 17, 16, 24, and 5 CYP families were predominant, while the domain Archaea was represented by CYP119A1. The phylum Cyanobacteria has two families, while 23 actinobacterial CYPs (other than Streptomyces and Mycobacterium) were also detected. The detected prokaryote CYPs are responsible for biodegradation of camphor, hydroxylation of monoterpene alcohols, biosynthesis of secondary metabolites, and hydroxylation of fatty acids and steroidal compounds. The eukaryote CYPome was represented by seven fungal CYPs (CYP505A3, CYP505B1, CYP51A, CYP51C, CYP55A1, CYP55A2, and CYP55A3) from Acremonium egyptiacum, Fusarium oxysporum, Aspergillus oryzae, Gibberella moniliformis, Aspergillus flavus, and Fusarium lichenicola, respectively, and CYP524A1 from the slime mold, Dictyostelium discoideum. The fungi CYPs were involved in biosynthesis of secondary metabolites, hydroxylation of fatty acids, and nitrate reduction and denitrification. Conclusions This study has established the diverse roles played by CYPs in soil, its implication for soil health and resilience, and its potentials for industrial application.

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Section: Discussionmentioning

confidence: 68%

Deciphering the cytochrome P450 genes in the microbiome of a chronically polluted soil with history of agricultural activities

et al. 2022

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“…Multiple sequence alignment of CYP107X1 with P450 Vdh from Pseudonocardia autotrophica , [26] P450 PikC from S. venezuelae , [27] CYP107W1 and CYP107L2 from S. avermitilis , [28,29] P450eryF from S. erythraea [30] and CYP107G1 from Streptomyces rapamycinicus [31] was performed to observe sequence conservation and the presence of the signature motif. The characteristic conserved dioxygen‐binding motif of the I‐helix and EXXR motif of the K helix for the P450 family were observed ( Figure 1).…”

Section: Resultsmentioning

confidence: 99%

The 16α‐Hydroxylation of Progesterone by Cytochrome P450 107X1 from Streptomyces avermitilis

Lin

Gao

et al. 2022

Chemistry & Biodiversity

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Cytochrome P450 enzymes (CYPs or P450s) are ubiquitous heme‐dependent enzymes that catalyze the monooxygenation of non‐activated C−H bonds to modify the structure of the substrate. In this study, we heterologously expressed CYP107X1 from Streptomyces avermitilis and conducted in vitro substrate screening using the alternative redox partners putidaredoxin and putidaredoxin reductase. CYP107X1 catalyzed the 16α‐hydroxylation of progesterone with regio‐ and stereoselectivity. The spectroscopic analyses showed that CYP107X1 bound progesterone with a relatively high Kd value of 65.3±38.9 μM. The Km and kcat values for progesterone were estimated to be 47.7±12.0 μM and 0.30 min−1, respectively. Furthermore, a crystal structure was obtained of CYP107X1 bound with glycerol from the buffer solution. Interestingly, a conserved threonine was replaced with asparagine in CYP107X1, indicating that it may adopt an unnatural proton transfer process and play a crucial role in its catalytic activity.

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“…CYP107 family members can function as oxidative tailoring enzymes in macrolide antibiotic biosynthetic pathways, such as those generating erythromycin and mycinamicin [18,19]. In Streptomyces species, CYP107 family members are involved in the biosynthesis of many valuable human antibiotics, including pikromycin and rapamycin [20,21]. CYP107H1 (P450BioI), found in Bacillus subtilis, synthesizes pimelic acid, a major component of biotin (vitamin B7) [22].…”

Section: Introductionmentioning

confidence: 99%

Structure–Function Analysis of the Biotechnologically Important Cytochrome P450 107 (CYP107) Enzyme Family

Padayachee,

Lamb,

Nelson

et al. 2023

Biomolecules

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Cytochrome P450 monooxygenases (CYPs; P450s) are a superfamily of heme-containing enzymes that are recognized for their vast substrate range and oxidative multifunctionality. CYP107 family members perform hydroxylation and epoxidation processes, producing a variety of biotechnologically useful secondary metabolites. Despite their biotechnological importance, a thorough examination of CYP107 protein structures regarding active site cavity dynamics and key amino acids interacting with bound ligands has yet to be undertaken. To address this research knowledge gap, 44 CYP107 crystal structures were investigated in this study. We demonstrate that the CYP107 active site cavity is very flexible, with ligand binding reducing the volume of the active site in some situations and increasing volume size in other instances. Polar interactions between the substrate and active site residues result in crucial salt bridges and the formation of proton shuttling pathways. Hydrophobic interactions, however, anchor the substrate within the active site. The amino acid residues within the binding pocket influence substrate orientation and anchoring, determining the position of the hydroxylation site and hence direct CYP107’s catalytic activity. Additionally, the amino acid dynamics within and around the binding pocket determine CYP107’s multifunctionality. This study serves as a reference for understanding the structure–function analysis of CYP107 family members precisely and the structure–function analysis of P450 enzymes in general. Finally, this work will aid in the genetic engineering of CYP107 enzymes to produce novel molecules of biotechnological interest.

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Structural insights into CYP107G1 from rapamycin-producing Streptomyces rapamycinicus

Cited by 7 publications

References 28 publications

Deciphering the cytochrome P450 genes in the microbiome of a chronically polluted soil with history of agricultural activities

Deciphering the cytochrome P450 genes in the microbiome of a chronically polluted soil with history of agricultural activities

The 16α‐Hydroxylation of Progesterone by Cytochrome P450 107X1 from Streptomyces avermitilis

Structure–Function Analysis of the Biotechnologically Important Cytochrome P450 107 (CYP107) Enzyme Family

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