Structural and Functional Trends in Dehydrating Bimodules from trans-Acyltransferase Polyketide Synthases

Abstract

SUMMARY In an effort to uncover the structural motifs and biosynthetic logic of the relatively uncharacterized trans-acyltransferase polyketide synthases, we have begun the dissection of the enigmatic dehydrating bimodules common in these enzymatic assembly lines. We report the 1.98 Å-resolution structure of a ketoreductase (KR) from the first half of a type A dehydrating bimodule and the 2.22 Å-resolution structure of a dehydratase (DH) from the second half of a type B dehydrating bimodule. The KR, from the third module of the bacillaene synthase, and the DH, from the tenth module of the difficidin synthase, possess features not observed in structurally-characterized homologs. The DH architecture provides clues for how it catalyzes a unique double dehydration. Correlations between the chemistries proposed for dehydrating bimodules and bioinformatic analysis indicate that type A dehydrating bimodules generally produce an α/β-cis alkene moiety while type B dehydrating bimodules generally produce an α/β-trans, γ/δ-cis diene moiety.

The modules of trans‐acyltransferase assembly lines redefined with a central acyl carrier protein

“…The KR I clade contains KRs that are from methyltransferase (MT)‐less modules and generally A‐type (A‐type KRs generate l ‐β‐hydroxy groups), the KR II contains KRs that are from MT‐less modules and generally B‐type (B‐type KRs generate d ‐β‐hydroxy groups), the KR III clade contains KRs that are from MT‐containing modules and can be A‐type or B‐type, and the KR IV clade contains KRs that are from the first module of dehydrating bimodules as well as some α‐oxidizing modules and are A‐type. The structural biology of KRs supports these clade divisions (KR II , MlnKR7, PDB 5D2E; KR IV , PksKR4, PDB 5KTK) …”

“…The C domain encoded by BasC apparently substitutes for the second KS of type B dehydrating bimodules. Interestingly, this C domain and a TE that makes an equivalent substitution in the macrolactin assembly line both gatekeep for a cis‐α/β, trans‐γ/δ diene in contrast to the trans‐α/β, cis‐γ/δ diene normally selected by type B dehydrating bimodules (the dienes may be interconverted by DH) …”

Characterization of the biosynthetic gene cluster for cryptic phthoxazolin A in Streptomyces avermitilis

“…In particular, PKS modules 8 and 9 include the interesting feature of a non-elongating KS (KS 0 ) domain. These modules are composed of KS-KR-ACP-KS 0 domains followed by DH-ACP domains, and are grouped as type A bimodules for dehydration [ 14 , 42 ] In addition, the domain pair of KS 0 -ACP as a non-elongating module is also embedded in PKS module 11. Both the type A bimodule for dehydration and the domain pair of KS 0 -ACP are ubiquitously found in the trans -AT type I PKS system [ 14 ].…”

Dehydration reactions in polyfunctional natural products

“…25 Other examples of double dehydrations are seen in trans-acyltransferase polyketide synthases where dehydrating bi-modules are responsible for installing an a/b-trans, g/d-cis diene in the difficidin biosynthesis. 26 The identification of a predicted protease, PynH, performing dehydration of a serine side-chain to an exo-methylene moiety in the biosynthesis of the pyranonigrins has also been reported. 27 Scheme 4: A) Sulfene formation from methanesulfonyl chloride (9) by dehydrohalogenation generates a highly reactive sulfonylating agent.…”