5INI

Structural basis for acyl-CoA carboxylase-mediated assembly of unusual polyketide synthase extender units incorporated into the stambomycin antibiotics

Summary for 5INI

• Entry DOI: 10.2210/pdb5ini/pdb
• Related: 5INF 5ING
• Descriptor: Putative carboxyl transferase, HEXANOYL-COENZYME A (3 entities in total)
• Functional Keywords: polyketide, acyl-coa, crotonase, extender-unit, transferase
• Biological source: Streptomyces ambofaciens ATCC 23877
• Total number of polymer chains: 6
• Total formula weight: 352066.55

Authors

Valentic, T.R.,Ray, L.,Miyazawa, T.,Withall, D.M.,Song, L.,Milligan, J.C.,Osada, H.,Tsai, S.C.,Challis, G.L. (deposition date: 2016-03-07, release date: 2016-12-28, Last modification date: 2023-09-27)

Primary citation

Ray, L.,Valentic, T.R.,Miyazawa, T.,Withall, D.M.,Song, L.,Milligan, J.C.,Osada, H.,Takahashi, S.,Tsai, S.C.,Challis, G.L.
A crotonyl-CoA reductase-carboxylase independent pathway for assembly of unusual alkylmalonyl-CoA polyketide synthase extender units.
Nat Commun, 7:13609-13609, 2016

PubMed Abstract: 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.

PubMed: 28000660
DOI: 10.1038/ncomms13609

Experimental method

X-RAY DIFFRACTION (2.85 Å)