Cryogenic X-ray crystal structure analysis for the complex of scytalone dehydratase of a rice blast fungus and its tight-binding inhibitor, carpropamid: the structural basis of tight-binding inhibition

Biochemistry. 1998 Jul 14;37(28):9931-9. doi: 10.1021/bi980321b.

Abstract

Scytalone dehydratase is a member of the group of enzymes involved in fungal melanin biosynthesis in a phytopathogenic fungus, Pyricularia oryzae, which causes rice blast disease. Carpropamid [(1RS,3SR)-2, 2-dichloro-N-[(R)-1-(4-chlorophenyl)ethyl]-1-ethyl-3-methylcyclopropa necarboxamide] is a tight-binding inhibitor of the enzyme. To clarify the structural basis for tight-binding inhibition, the crystal structure of the enzyme complexed with carpropamid was analyzed using diffraction data collected at 100 K. The structural model was refined to a crystallographic R-factor of 0.180 against reflections up to a resolution of 2.1 A. Carpropamid was bound in a hydrophobic cavity of the enzyme. Three types of interactions appeared to contribute to the binding. (i) A hydrogen bond was formed between a chloride atom in the dichloromethylethylcyclopropane ring of carpropamid and Asn-131 of the enzyme. (ii) The (chlorophenyl)ethyl group of carpropamid built strong contacts with Val-75, and this group further formed a cluster of aromatic rings together with four aromatic residues in the enzyme (Tyr-50, Phe-53, Phe-158, and Phe-162). (iii) Two hydration water molecules bound to the carboxamide group of carpropamid, and they were further hydrogen-bonded to Tyr-30, Tyr-50, His-85, and His-110. As a result of interactions between carpropamid and the phenylalanine residues (Phe-158 and Phe-162) in the C-terminal region of the enzyme, the C-terminal region completely covered the inhibitor, ensuring its localization in the cavity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amides / chemistry*
  • Amides / pharmacology
  • Amino Acids / chemistry
  • Binding, Competitive
  • Crystallography, X-Ray
  • Cyclopropanes / chemistry*
  • Cyclopropanes / pharmacology
  • Freezing
  • Fungicides, Industrial / chemistry*
  • Fungicides, Industrial / pharmacology
  • Hydro-Lyases / antagonists & inhibitors
  • Hydro-Lyases / chemistry*
  • Hydro-Lyases / metabolism
  • Macromolecular Substances
  • Mitosporic Fungi / enzymology*
  • Models, Molecular
  • Oryza / microbiology*
  • Peptide Fragments / antagonists & inhibitors
  • Peptide Fragments / chemistry
  • Peptide Fragments / metabolism
  • Protein Binding
  • Structure-Activity Relationship

Substances

  • Amides
  • Amino Acids
  • Cyclopropanes
  • Fungicides, Industrial
  • Macromolecular Substances
  • Peptide Fragments
  • Hydro-Lyases
  • scytalone dehydratase
  • carpropamid

Associated data

  • PDB/2STD