4DK4

Crystal Structure of Trypanosoma brucei dUTPase with dUpNp, Ca2+ and Na+

Summary for 4DK4

• Entry DOI: 10.2210/pdb4dk4/pdb
• Related: 4DK2 4DKB 4DL8 4DLC
• Descriptor: Deoxyuridine triphosphatase, 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: all alpha ntp pyrophosphohydrolase, all alpha ntp pyrophosphatase, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Trypanosoma brucei
• Total number of polymer chains: 2
• Total formula weight: 65389.19

Authors

Hemsworth, G.R.,Gonzalez-Pacanowska, D.,Wilson, K.S. (deposition date: 2012-02-03, release date: 2013-08-07, Last modification date: 2023-09-13)

Primary citation

Hemsworth, G.R.,Gonzalez-Pacanowska, D.,Wilson, K.S.
On the catalytic mechanism of dimeric dUTPases.
Biochem.J., 456:81-88, 2013

PubMed Abstract: The Tritryps Trypanosoma brucei, Trypanosoma cruzi and Leishmania donovani are responsible for great morbidity and mortality in developing countries. Their dimeric dUTPases are members of the all-α NTP pyrophosphohydrolase family and represent promising drug targets due to their essential nature and markedly different structural and biochemical properties compared with the trimeric human enzyme. In the present paper we describe the structure of the T. brucei enzyme in open and closed conformations. Furthermore, we probe the reaction mechanism through the binding of transition state mimics both in solution and in the crystal. 31P-NMR and tryptophan fluorescence quenching in the presence of AlF3 and MgF3- identified which phosphate is subject to nucleophilic attack by a water molecule. The structures in complex with two transition state analogues confirm that the nucleophilic attack occurs on the β-phosphate in contrast with the α-phosphate in the trimeric enzymes. These results establish the structural basis of catalysis of these important housekeeping enzymes and has ramifications for the wider all-α NTP pyrophosphohydrolase family.

PubMed: 24001052
DOI: 10.1042/BJ20130796

Experimental method

X-RAY DIFFRACTION (1.9 Å)