A crotonyl-CoA reductase-carboxylase independent pathway for assembly of unusual alkylmalonyl-CoA polyketide synthase extender units

Nat Commun. 2016 Dec 21;7:13609. doi: 10.1038/ncomms13609.


Type I modular polyketide synthases assemble diverse bioactive natural products. Such multienzymes typically use malonyl and methylmalonyl-CoA building blocks for polyketide chain assembly. However, in several cases more exotic alkylmalonyl-CoA extender units are also known to be incorporated. In all examples studied to date, such unusual extender units are biosynthesized via reductive carboxylation of α, β-unsaturated thioesters catalysed by crotonyl-CoA reductase/carboxylase (CCRC) homologues. Here we show using a chemically-synthesized deuterium-labelled mechanistic probe, and heterologous gene expression experiments that the unusual alkylmalonyl-CoA extender units incorporated into the stambomycin family of polyketide antibiotics are assembled by direct carboxylation of medium chain acyl-CoA thioesters. X-ray crystal structures of the unusual β-subunit of the acyl-CoA carboxylase (YCC) responsible for this reaction, alone and in complex with hexanoyl-CoA, reveal the molecular basis for substrate recognition, inspiring the development of methodology for polyketide bio-orthogonal tagging via incorporation of 6-azidohexanoic acid and 8-nonynoic acid into novel stambomycin analogues.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acyl Coenzyme A / chemistry
  • Acyl Coenzyme A / genetics
  • Acyl Coenzyme A / metabolism*
  • Acyl-CoA Dehydrogenases / metabolism
  • Amino Acid Sequence
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Carbon-Carbon Ligases / metabolism
  • Crystallography, X-Ray
  • Models, Molecular
  • Molecular Structure
  • Polyketide Synthases / chemistry
  • Polyketide Synthases / genetics
  • Polyketide Synthases / metabolism*
  • Polyketides / chemistry
  • Polyketides / metabolism*
  • Protein Conformation
  • Sequence Homology, Amino Acid
  • Streptomyces / genetics
  • Streptomyces / metabolism
  • Substrate Specificity


  • Acyl Coenzyme A
  • Bacterial Proteins
  • Polyketides
  • methylmalonyl-coenzyme A
  • Polyketide Synthases
  • Acyl-CoA Dehydrogenases
  • acyl-CoA dehydrogenase (NADP+)
  • Carbon-Carbon Ligases
  • acyl-CoA carboxylase