Solution structure and proposed domain domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase

Protein Sci. 2007 Oct;16(10):2093-107. doi: 10.1110/ps.073011407.

Abstract

Polyketides are a medicinally important class of natural products. The architecture of modular polyketide synthases (PKSs), composed of multiple covalently linked domains grouped into modules, provides an attractive framework for engineering novel polyketide-producing assemblies. However, impaired domain-domain interactions can compromise the efficiency of engineered polyketide biosynthesis. To facilitate the study of these domain-domain interactions, we have used nuclear magnetic resonance (NMR) spectroscopy to determine the first solution structure of an acyl carrier protein (ACP) domain from a modular PKS, 6-deoxyerythronolide B synthase (DEBS). The tertiary fold of this 10-kD domain is a three-helical bundle; an additional short helix in the second loop also contributes to the core helical packing. Superposition of residues 14-94 of the ensemble on the mean structure yields an average atomic RMSD of 0.64 +/- 0.09 Angstrom for the backbone atoms (1.21 +/- 0.13 Angstrom for all non-hydrogen atoms). The three major helices superimpose with a backbone RMSD of 0.48 +/- 0.10 Angstrom (0.99 +/- 0.11 Angstrom for non-hydrogen atoms). Based on this solution structure, homology models were constructed for five other DEBS ACP domains. Comparison of their steric and electrostatic surfaces at the putative interaction interface (centered on helix II) suggests a model for protein-protein recognition of ACP domains, consistent with the previously observed specificity. Site-directed mutagenesis experiments indicate that two of the identified residues influence the specificity of ACP recognition.

Publication types

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

MeSH terms

  • Acyl Carrier Protein / chemistry*
  • Amino Acid Sequence
  • Bacterial Proteins
  • Binding Sites
  • Cytochrome P-450 Enzyme System / chemistry*
  • Cytochrome P-450 Enzyme System / classification
  • Cytochrome P-450 Enzyme System / genetics
  • Lactones / chemistry
  • Mixed Function Oxygenases / chemistry*
  • Mixed Function Oxygenases / classification
  • Mixed Function Oxygenases / genetics
  • Models, Molecular*
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular
  • Phylogeny
  • Point Mutation
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Solutions
  • Static Electricity
  • Structural Homology, Protein

Substances

  • Acyl Carrier Protein
  • Bacterial Proteins
  • Lactones
  • Solutions
  • Cytochrome P-450 Enzyme System
  • Mixed Function Oxygenases
  • eryF protein, Saccharopolyspora erythraea