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One site fits both: A model for the ternary complex of folate + NADPH in R67 dihydrofolate reductase, a D2 symmetric enzyme

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Abstract

R67 dihydrofolate reductase (DHFR) is a novel enzyme that confers resistance to the antibiotic trimethoprim. The crystal structure of R67 DHFR displays a toroidal structure with a central active-site pore. This homotetrameric protein exhibits 222 symmetry, with only a few residues from each chain contributing to the active site, so related sites must be used to bind both substrate (dihydrofolate) and cofactor (NADPH) in the productive R67 DHFR•NADPH•dihydrofolate complex. Whereas the site of folate binding has been partially resolved crystallographically, an interesting question remains: how can the highly symmetrical active site also bind and orient NADPH for catalysis? To model this ternary complex, we employed DOCK and SLIDE, two methods for docking flexible ligands into proteins using quite different algorithms. The bound pteridine ring of folate (Fol I) from the crystal structure of R67 DHFR was used as the basis for docking the nicotinamide-ribose-Pi (NMN) moiety of NADPH. NMN was positioned by both DOCK and SLIDE on the opposite side of the pore from Fol I, where it interacts with Fol I at the pore's center. Numerous residues serve dual roles in binding. For example, Gln 67 from both the B and D subunits has several contacts with the pteridine ring, while the same residue from the A and C subunits has several contacts with the nicotinamide ring. The residues involved in dual roles are generally amphipathic, allowing them to make both hydrophobic and hydrophilic contacts with the ligands. The result is a `hot spot' binding surface allowing the same residues to co-optimize the binding of two ligands, and orient them for catalysis.

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Authors and Affiliations

  1. Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996-0840, USA

    Elizabeth E. Howell, Ushma Shukla, Stephanie N. Hicks & R. Derike Smiley

  2. Protein Structural Analysis and Design Laboratory, Department of Biochemistry and Molecular Biology, and Center for Biological Modeling, Michigan State University, East Lansing, MI, 48824, USA

    Leslie A. Kuhn

  3. Protein Structural Analysis and Design Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA

    Maria I. Zavodszky

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  1. Elizabeth E. Howell
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Howell, E.E., Shukla, U., Hicks, S.N. et al. One site fits both: A model for the ternary complex of folate + NADPH in R67 dihydrofolate reductase, a D2 symmetric enzyme. J Comput Aided Mol Des 15, 1035–1052 (2001). https://doi.org/10.1023/A:1014824725891

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