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.
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.
Nakasako
M
M
The Institute of Physical and Chemical Research (RIKEN), Saitama, Japan.
Motoyama
T
T
Kurahashi
Y
Y
Yamaguchi
I
I
D000577:Amides / Q000737:chemistry* / Q000494:pharmacology; D000596:Amino Acids / Q000737:chemistry; D001667:Binding, Competitive; D018360:Crystallography, X-Ray; D003521:Cyclopropanes / Q000737:chemistry* / Q000494:pharmacology; D005615:Freezing; D005659:Fungicides, Industrial / Q000737:chemistry* / Q000494:pharmacology; D006836:Hydro-Lyases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D046911:Macromolecular Substances; D003904:Mitosporic Fungi / Q000201:enzymology*; D008958:Models, Molecular; D012275:Oryza / Q000382:microbiology*; D010446:Peptide Fragments / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D013329:Structure-Activity Relationship
D000577:Amides; D000596:Amino Acids; D003521:Cyclopropanes; D005659:Fungicides, Industrial; D046911:Macromolecular Substances; D010446:Peptide Fragments; D006836:Hydro-Lyases; C082741:scytalone dehydratase; C113565:carpropamid