Please contact us for any questions or request for reagents for this structure.

Human Dihydropyrimidinase

Click on the iSee icon to launch an enhanced annotation with interactive 3D representations and animated transitions. Please note that a web plugin (activeICM) is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available.

PDB Code 2VR2 Target Class Oxidoreductases Target DHP Alias DHP, DHPase, DPYS Disease Area/Function drug metabolism and toxicology Date Deposited Mar 25 2008 Authors M.WELIN, T.KARLBERG, J.ANDERSSON, C.H.ARROWSMITH, H.BERGLUND, R.D.BUSAM, R.COLLINS, L.G.DAHLGREN, A.M.EDWARDS, S.FLODIN, A.FLORES, S.GRASLUND, M.HAMMARSTROM, M.D.HERMAN, I.JOHANSSON, A.KALLAS, T.KOTENYOVA, L.LEHTIO, M.MOCHE, M.E.NILSSON, T.NYMAN, C.PERSSON, J.SAGEMARK, L.SVENSSON, A.G.THORSELL, L.TRESAUGUES, S.VAN DEN BERG, J.WEIGELT, M.WIKSTROM, P.NORDLUND

About this structure

Dihydropyrimidinase (DHPase, E.C. 3.5.2.2) is involved in the reductive degradation of uracil and thymine and in addition several anti-cancer drugs. It catalyses the second of the three steps in the pathway, the hydrolysis of 5,6-dihydrouracil and 5,6-dihydrothymine to the corresponding N-carbamoyl -amino acids [1]. The first and third steps are carried out by dihydropyrimidine dehydrogenase and beta-ureidopropionase respectively. DHPase can activate the prodrug dexrazoxane to its active form ADR-925, which is used to reduce cardio toxicity of the DNA interacting drug, doxorubicin [2].

DHPases are homotetrameric metalloenzymes binding Zn2+. The subunit structure consists of two domains, a core catalytic domain and a -sandwich domain [1]. Several point mutations have been shown to give decreased activity of DHPase, which can lead to dihydropyrimidinuria, which is a very rare disease with symptoms like, seizures, mental retardation, growth retardation, and dysmorphic features [3,4].

Here we present the structure of the human DHPase to a resolution of 2.8 Å. The structure was solved with molecular replacement using the DHPase from Dictyostelium discoideum (pdb-code: 2FTW). Protein crystals were obtained in the presence of chymotrypsin [5] and the most probable sequence in the crystal structure is Ala2-Leu500 determined by MS of protein proteolysed over night. Two Zn2+ ions are found in the active site of the structure. There is only one molecule in the asymmetric unit, but the whole tetramer can be build using symmetry operations. Structural information concerning the human DHPase will give insights into the features of the point mutations giving a deficient enzyme leading to dihydropyrimidinuria.

References

  1. Schnackerz KD, Dobritzsch D. Amidohydrolases of the reductive pyrimidine catabolic pathway Purification, characterization, structure, reaction mechanisms and enzyme deficiency. Biochim Biophys Acta. 2008 Mar;1784(3):431-44.
  2. Schroeder PE, Hasinoff BB. The doxorubicin-cardioprotective drug dexrazoxane undergoes metabolism in the rat to its metal ion-chelating form ADR-925. Cancer Chemother Pharmacol. 2002 Dec;50(6):509-13.
  3. Hamajima N. et al. (1998). Dihydropyrimidinase deficiency: structural organization, chromosomal localization, and mutation analysis of the human dihydropyrimidinase gene. Am J Hum Genet. 1998 Sep;63(3):717-26.
  4. van Gennip, A. H., de Abreu, R. A., van Lenthe, H., Bakkeren, J., Rotteveel, J., Vreken, P., and van Kuilenburg, A. B. (1997) J. Inherit. Metab. Dis. 20, 339–342
  5. Dong A. et al. In situ proteolysis for protein crystallization and structure determination. Nat Methods. 2007 Dec;4(12):1019-21.