Recent advances in the structural biology of modular polyketide synthases and nonribosomal peptide synthetases

Katsuyama, Yoshihiko; Miyanaga, Akimasa

doi:10.1016/j.cbpa.2022.102223

Cited by 9 publications

(3 citation statements)

References 53 publications

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“…The crosslinked complex forms a symmetric dimer structure in which the two ACP L domains bind to the KS Q domain dimer, suggesting that in a KS Q –AT L –ACP L loading module, the two ACP L domains could simultaneously shuttle to the catalytic domains (Figure S20A). Although several PKS modules have different domain organizations, only the structures of full-length modules consisting of KS–AT–KR–ACP have been determined. ,,, As a dynamic property of a KS–AT–KR–ACP module, it is proposed that the dimeric KS–AT–KR–ACP module adopts an asymmetric conformation with the binding of a single ACP domain to the KS homodimer when the KS domain functions (Figure S20B). An artificial state that is crosslinked with the separated ACP L domain may cause a symmetric conformation of the GfsA loading module.…”

Section: Resultsmentioning

confidence: 99%

Structure-Based Analysis of Transient Interactions between Ketosynthase-like Decarboxylase and Acyl Carrier Protein in a Loading Module of Modular Polyketide Synthase

et al. 2023

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Ketosynthase-like decarboxylase (KS Q ) domains are widely distributed in the loading modules of modular type I polyketide synthases (PKSs) and catalyze the decarboxylation of the (alkyl-)malonyl unit bound to the acyl carrier protein (ACP) in the loading module for the construction of the PKS starter unit. Previously, we performed a structural and functional analysis of the GfsA KS Q domain involved in the biosynthesis of macrolide antibiotic FD-891. We furthermore revealed the recognition mechanism for the malonic acid thioester moiety of the malonyl-GfsA loading module ACP (ACP L ) as a substrate. However, the exact recognition mechanism for the GfsA ACP L moiety remains unclear. Here, we present a structural basis for the interactions between the GfsA KS Q domain and GfsA ACP L . We determined the crystal structure of the GfsA KS Qacyltransferase (AT) didomain in complex with ACP L (ACP L =KS Q AT complex) by using a pantetheine crosslinking probe. We identified the key amino acid residues involved in the KS Q domain−ACP L interactions and confirmed the importance of these residues by mutational analysis. The binding mode of ACP L to the GfsA KS Q domain is similar to that of ACP to the ketosynthase domain in modular type I PKSs. Furthermore, comparing the ACP L =KS Q AT complex structure with other full-length PKS module structures provides important insights into the overall architectures and conformational dynamics of the type I PKS modules.

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Section: Resultsmentioning

confidence: 99%

Structure-Based Analysis of Transient Interactions between Ketosynthase-like Decarboxylase and Acyl Carrier Protein in a Loading Module of Modular Polyketide Synthase

et al. 2023

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“…As an alternative to chemical synthesis, biosynthetic engineering proves to be an effective method for producing structural varieties of natural products, especially polyketides and non-ribosomal peptides which are assembled in a modular fashion [ [4] , [5] , [6] , [7] ]. However, the success of these approaches depends on the understanding of the biosynthetic mechanism and the achievement of a sufficient production titer of products, as engineering of biosynthetic genes usually reduces the yield.…”

Section: Introductionmentioning

confidence: 99%

Analyzing and engineering of the biosynthetic pathway of mollemycin A for enhancing its production

Jin,

Chen,

Zhang

et al. 2024

Synthetic and Systems Biotechnology

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“…39 As NRPS adenylation domains serve as "gatekeepers" for the selection of starter substrates, they have been attractive targets for engineering for the development of novel natural products with therapeutic potential. 40 These studies integrate structural information to enhance the rational engineering of adenylation domains that can incorporate substrate analogs to generate new products. Point mutations in EntE from enterobactin biosynthesis have expanded the binding pocket to tolerate a diverse range of benzoic acid analogs.…”

Section: Introductionmentioning

confidence: 99%

Expanding the substrate selectivity of the fimsbactin biosynthetic adenylation domain, FbsH

Ahmed,

Balutowski,

Yang

et al. 2024

Preprint

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Nonribosomal peptide synthetases (NRPSs) produce diverse natural products including siderophores, chelating agents that many pathogenic bacteria produce to survive in low iron conditions. Engineering NRPSs to produce diverse siderophore analogs could lead to the generation of novel antibiotics and imaging agents that take advantage of this unique iron uptake system in bacteria. The highly pathogenic and antibiotic-resistant bacteria Acinetobacter baumannii produces fimsbactin, an unusual branched siderophore with iron-binding catechol groups bound to a serine or threonine side chain. To explore the substrate promiscuity of the assembly line enzymes, we report a structure-guided investigation of the stand-alone aryl adenylation enzyme FbsH. We report on structures bound to its native substrate 2,3-dihydroxybenzoic acid (DHB) as well as an inhibitor that mimics the adenylate intermediate. We produced enzyme variants with an expanded binding pocket that are more tolerant for analogs containing a DHB C4 modification. Wild-type and mutant enzymes were then used in an in vitro reconstitution analysis to assess the production of analogs of the final product as well as several early-stage intermediates. This analysis shows that some altered substrates progress down the fimsbactin assembly line to the downstream domains. However, analogs from alternate building blocks are produced at lower levels, indicating that selectivity exists in the downstream catalytic domains. These findings expand the substrate scope of producing condensation products between serine and aryl acids and identify the bottlenecks for chemoenzymatic production of fimsbactin analogs.

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Recent advances in the structural biology of modular polyketide synthases and nonribosomal peptide synthetases

Cited by 9 publications

References 53 publications

Structure-Based Analysis of Transient Interactions between Ketosynthase-like Decarboxylase and Acyl Carrier Protein in a Loading Module of Modular Polyketide Synthase

Structure-Based Analysis of Transient Interactions between Ketosynthase-like Decarboxylase and Acyl Carrier Protein in a Loading Module of Modular Polyketide Synthase

Analyzing and engineering of the biosynthetic pathway of mollemycin A for enhancing its production

Expanding the substrate selectivity of the fimsbactin biosynthetic adenylation domain, FbsH

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