1GTH

DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND 5-IODOURACIL

Summary for 1GTH

• Entry DOI: 10.2210/pdb1gth/pdb
• Related: 1GT8 1GTE 1H7W 1H7X
• Descriptor: DIHYDROPYRIMIDINE DEHYDROGENASE, IRON/SULFUR CLUSTER, FLAVIN MONONUCLEOTIDE, ... (9 entities in total)
• Functional Keywords: electron transfer, flavin, iron-sulfur clusters, pyrimidine catabolism, 5-fluorouracil degradation, oxidoreductase
• Biological source: SUS SCROFA (PIG)
• Total number of polymer chains: 4
• Total formula weight: 460818.94

Authors

Dobritzsch, D.,Ricagno, S.,Schneider, G.,Schnackerz, K.D.,Lindqvist, Y. (deposition date: 2002-01-15, release date: 2002-04-11, Last modification date: 2024-05-01)

Primary citation

Dobritzsch, D.,Ricagno, S.,Schneider, G.,Schnackerz, K.D.,Lindqvist, Y.
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., 277:13155-13166, 2002

PubMed 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.

PubMed: 11796730
DOI: 10.1074/jbc.M111877200

Experimental method

X-RAY DIFFRACTION (2.25 Å)