PPubMed1 Jan 2022Cited 2×

The crystal structure of DynF from the dynemicin-biosynthesis pathway of <i> Micromonospora chersina </i> DynF

Abigael J. Kosgei, Mitchell D. Miller, Minakshi Bhardwaj, Weijun Xu, Jon S. Thorson, Steven G. Van Lanen, George N. Phillips Jr

Abstract

The crystal structure of DynF was determined to a resolution of 1.50 Å, revealing a dimeric eight-stranded β-barrel structure with palmitic acid bound in the interior.

A figure from The crystal structure of DynF from the dynemicin-biosynthesis pathway of <i> Micromonospora chersina </i> DynF — fig. from the paper

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Crystal structure of DynF at 1.5 Å reveals a novel eight‑stranded β‑barrel dimer that binds palmitic acid, suggesting a role in handling dynemicin polyene intermediates.

What’s new

i.Determined DynF crystal structure to 1.50 Å with Rwork=0.16, Rfree=0.19
ii.Identified DynF as a novel eight‑stranded antiparallel β‑barrel fold lacking known homologs
iii.Showed DynF forms a stable dimer in the crystal and possibly in solution
iv.Discovered an endogenous palmitic‑acid ligand inside the barrel
v.Provided structural basis for hypothesizing DynF’s role in binding dynemicin biosynthetic intermediates

How they did it

DynF was purified and crystallized, and X‑ray diffraction data were collected to 1.50 Å resolution; the structure was solved and refined, with PISA analysis used to assess oligomeric state. Size‑exclusion chromatography evaluated solution oligomerization, and GC‑MS identified the bound ligand as palmitic acid. Co‑expression with pathway enzymes tested alternative ligands.

What they found

Structure resolved at 1.50 Å (Rwork=0.16, Rfree=0.19)
DynF forms a dimer in the crystal and may exist in higher oligomeric states in solution
Eight‑stranded antiparallel β‑barrel represents a novel protein fold (Z‑score <10, <15% identity)
Electron density revealed an elongated ligand identified as palmitic acid by GC‑MS
Co‑expression with PKS genes did not change the ligand profile, still showing palmitic acid

Caveats

✕Functional role of DynF remains unconfirmed; ligand may be a contaminant from E. coli
✕No biochemical assays demonstrating binding or processing of native biosynthetic intermediates
✕Low structural similarity to known proteins limits functional inference
✕Co‑expression experiments did not capture the presumed polyene substrate

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The crystal structure of DynF from the dynemicin-biosynthesis pathway of <i> Micromonospora chersina </i> DynF

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