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TitleAncestral sequence reconstruction as a tool for structural analysis of modular polyketide synthases.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 6847, Year 2025
Publish dateJul 25, 2025
AuthorsTaichi Chisuga / Shota Takinami / Zengwei Liao / Masayuki Karasawa / Naruhiko Adachi / Masato Kawasaki / Toshio Moriya / Toshiya Senda / Tohru Terada / Fumitaka Kudo / Tadashi Eguchi / Shogo Nakano / Sohei Ito / Akimasa Miyanaga /
PubMed AbstractModular polyketide synthases (PKSs) are large multi-domain enzymes critical for the biosynthesis of polyketide antibiotics. However, challenges with structural analysis limits our mechanistic ...Modular polyketide synthases (PKSs) are large multi-domain enzymes critical for the biosynthesis of polyketide antibiotics. However, challenges with structural analysis limits our mechanistic understanding of modular PKSs. In this report, we explore the potential of ancestral sequence reconstruction (ASR) for structure analysis of target proteins. As a model, we focus on the FD-891 PKS loading module composed of ketosynthase-like decarboxylase (KS), acyltransferase (AT) and acyl carrier protein (ACP) domains. We construct a KSAncAT chimeric didomain by replacing the native AT with an ancestral AT (AncAT) using ASR. After confirming that KSAncAT chimeric didomain retains similar enzymatic function to the native KSAT didomain, we successfully determine a high-resolution crystal structure of the KSAncAT chimeric didomain and cryo-EM structures of the KS-ACP complex. These cryo-EM structures, which could not be determined for the native protein, exemplify the utility of ASR to enable cryo-EM single-particle analysis. Our findings demonstrate that integrating ASR with structural analysis provides deeper mechanistic insight into modular PKSs. Furthermore, applying ASR to a partial region of the targeted multi-domain proteins could expand the potential of ASR and may serve as a valuable framework for investigating the structure and function of various multi-domain proteins.
External linksNat Commun / PubMed:40715098 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2 - 2.73 Å
Structure data

EMDB-60989: Class 2 state of the GfsA KSQ-ancestralAT chimeric didomain in complex with the GfsA ACP domain
Method: EM (single particle) / Resolution: 2.73 Å

61520

9jj9

EMDB-61520, PDB-9jj9:
Class 3 state of the GfsA KSQ-ancestralAT chimeric didomain in complex with the GfsA ACP domain
Method: EM (single particle) / Resolution: 2.71 Å

61522

9jjb

EMDB-61522, PDB-9jjb:
Class 1 state of the GfsA KSQ-ancestralAT chimeric didomain in complex with the GfsA ACP domain
Method: EM (single particle) / Resolution: 2.68 Å

PDB-9iyw:
Crystal structure of chimeric KSQ-AT didomain
Method: X-RAY DIFFRACTION / Resolution: 2 Å

Chemicals

ChemComp-NA:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-9EF:
N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide

Source
  • streptomyces graminofaciens (bacteria)
  • synthetic construt (others)
KeywordsTRANSFERASE / Polyketide biosynthesis / Decarboxylase / Acyltransferase / Thiolase fold / LYASE / polyketide synthase

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