8HRV

dutpase of helicobacter pylori 26695

8HRV の概要

• エントリーDOI: 10.2210/pdb8hrv/pdb
• 分子名称: Deoxyuridine 5'-triphosphate nucleotidohydrolase, 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, MAGNESIUM ION, ... (5 entities in total)
• 機能のキーワード: complex, hydrolase
• 由来する生物種: Helicobacter pylori 26695 (Campylobacter pylori)
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 51702.68

構造登録者

Kumari, K.,Gourinath, S. (登録日: 2022-12-16, 公開日: 2024-01-17, 最終更新日: 2025-03-26)

主引用文献

Kumari, K.,Aggarwal, S.,Khan, F.M.,Munde, M.,Gourinath, S.
Structural analysis of dUTPase from Helicobacter pylori reveals unusual activity for dATP.
Int.J.Biol.Macromol., 282:136937-136937, 2024

PubMed Abstract: Helicobacter pylori deoxyuridine triphosphate nucleotidohydrolase (HpdUTPase) is a key enzyme in the synthesis of the thymidine nucleotide pathway. It catalyzes the hydrolysis of dUTP to dUMP and releases pyrophosphate. This enzyme has been shown to be essential in several pathogenic organisms. Here, we have determined the crystal structures of HpdUTPase in complex with α, β-imido dUTP (non-hydrolyzable substrate analog) and apo-state at resolution of 2 Å and 2.5 Å respectively. The flexible c terminal end of HpdUTPase which is not observed in apo-state structure and becomes ordered in the complex structure, suggesting its role in forming active site and substrate interaction. The Isothermal titration calorimetry (ITC) experiments reveal that hydrolysis of dUTP is an exothermic reaction with K = 35.0 ± 0.19 μM and the k = 1.20 ± 0.19 s. The ITC studies combined with MD simulations for all other nucleotides (dATP.dGTP, dCTP and dTTP) show that the active site of HpdUTPase strangely can also accommodate dATP. The structural comparison with the host (human) dUTPases reveals critical differences in substrate binding affinity of the active site of HpdUTPase. The detailed study suggests that the dATP binds in the active site of HpdUTPase making the number of preferable hydrogen bonds and shows activity with Km of 47 ± 2.4 μM.

PubMed: 39490855
DOI: 10.1016/j.ijbiomac.2024.136937

実験手法

X-RAY DIFFRACTION (2 Å)