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Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer.
J Biol Chem. 2002 Apr 12; 277(15):13155-66.JB

Abstract

Dihydroprymidine dehydrogenase catalyzes the first and rate-limiting step in pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds. The three-dimensional structures of a binary complex with the inhibitor 5-iodouracil and two ternary complexes with NADPH and the inhibitors 5-iodouracil and uracil-4-acetic acid were determined by x-ray crystallography. In the ternary complexes, NADPH is bound in a catalytically competent fashion, with the nicotinamide ring in a position suitable for hydride transfer to FAD. The structures provide a complete picture of the electron transfer chain from NADPH to the substrate, 5-iodouracil, spanning a distance of 56 A and involving FAD, four [Fe-S] clusters, and FMN as cofactors. The crystallographic analysis further reveals that pyrimidine binding triggers a conformational change of a flexible active-site loop in the alpha/beta-barrel domain, resulting in placement of a catalytically crucial cysteine close to the bound substrate. Loop closure requires physiological pH, which is also necessary for correct binding of NADPH. Binding of the voluminous competitive inhibitor uracil-4-acetic acid prevents loop closure due to steric hindrance. The three-dimensional structure of the ternary complex enzyme-NADPH-5-iodouracil supports the proposal that this compound acts as a mechanism-based inhibitor, covalently modifying the active-site residue Cys-671, resulting in S-(hexahydro-2,4-dioxo-5-pyrimidinyl)cysteine.

Authors+Show Affiliations

Division of Molecular Structural Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

11796730

Citation

Dobritzsch, Doreen, et al. "Crystal Structure of the Productive Ternary Complex of Dihydropyrimidine Dehydrogenase With NADPH and 5-iodouracil. Implications for Mechanism of Inhibition and Electron Transfer." The Journal of Biological Chemistry, vol. 277, no. 15, 2002, pp. 13155-66.
Dobritzsch D, Ricagno S, Schneider G, et al. Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer. J Biol Chem. 2002;277(15):13155-66.
Dobritzsch, D., Ricagno, S., Schneider, G., Schnackerz, K. D., & Lindqvist, Y. (2002). Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer. The Journal of Biological Chemistry, 277(15), 13155-66.
Dobritzsch D, et al. Crystal Structure of the Productive Ternary Complex of Dihydropyrimidine Dehydrogenase With NADPH and 5-iodouracil. Implications for Mechanism of Inhibition and Electron Transfer. J Biol Chem. 2002 Apr 12;277(15):13155-66. PubMed PMID: 11796730.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer. AU - Dobritzsch,Doreen, AU - Ricagno,Stefano, AU - Schneider,Gunter, AU - Schnackerz,Klaus D, AU - Lindqvist,Ylva, Y1 - 2002/01/16/ PY - 2002/1/18/pubmed PY - 2002/5/17/medline PY - 2002/1/18/entrez SP - 13155 EP - 66 JF - The Journal of biological chemistry JO - J Biol Chem VL - 277 IS - 15 N2 - Dihydroprymidine dehydrogenase catalyzes the first and rate-limiting step in pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds. The three-dimensional structures of a binary complex with the inhibitor 5-iodouracil and two ternary complexes with NADPH and the inhibitors 5-iodouracil and uracil-4-acetic acid were determined by x-ray crystallography. In the ternary complexes, NADPH is bound in a catalytically competent fashion, with the nicotinamide ring in a position suitable for hydride transfer to FAD. The structures provide a complete picture of the electron transfer chain from NADPH to the substrate, 5-iodouracil, spanning a distance of 56 A and involving FAD, four [Fe-S] clusters, and FMN as cofactors. The crystallographic analysis further reveals that pyrimidine binding triggers a conformational change of a flexible active-site loop in the alpha/beta-barrel domain, resulting in placement of a catalytically crucial cysteine close to the bound substrate. Loop closure requires physiological pH, which is also necessary for correct binding of NADPH. Binding of the voluminous competitive inhibitor uracil-4-acetic acid prevents loop closure due to steric hindrance. The three-dimensional structure of the ternary complex enzyme-NADPH-5-iodouracil supports the proposal that this compound acts as a mechanism-based inhibitor, covalently modifying the active-site residue Cys-671, resulting in S-(hexahydro-2,4-dioxo-5-pyrimidinyl)cysteine. SN - 0021-9258 UR - https://www.unboundmedicine.com/medline/citation/11796730/Crystal_structure_of_the_productive_ternary_complex_of_dihydropyrimidine_dehydrogenase_with_NADPH_and_5_iodouracil__Implications_for_mechanism_of_inhibition_and_electron_transfer_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0021-9258(20)85540-9 DB - PRIME DP - Unbound Medicine ER -