8I1I

Crystal structure of human MTH1(G2K/D120N mutant) in complex with 2-oxo-dATP at pH 7.7

Summary for 8I1I

• Entry DOI: 10.2210/pdb8i1i/pdb
• Descriptor: 7,8-dihydro-8-oxoguanine triphosphatase, [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate, SODIUM ION, ... (4 entities in total)
• Functional Keywords: nudix hydrolase, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 37168.54

Authors

Nakamura, T.,Yamagata, Y. (deposition date: 2023-01-13, release date: 2023-03-22, Last modification date: 2024-05-29)

Primary citation

Nakamura, T.,Koga-Ogawa, Y.,Fujimiya, K.,Chirifu, M.,Goto, M.,Ikemizu, S.,Nakabeppu, Y.,Yamagata, Y.
Protonation states of Asp residues in the human Nudix hydrolase MTH1 contribute to its broad substrate recognition.
Febs Lett., 597:1770-1778, 2023

PubMed Abstract: Human MutT homolog 1 (MTH1), also known as Nudix-type motif 1 (NUDT1), hydrolyzes 8-oxo-dGTP and 2-oxo-dATP with broad substrate recognition and has attracted attention in anticancer therapeutics. Previous studies on MTH1 have proposed that the exchange of the protonation state between Asp119 and Asp120 is essential for the broad substrate recognition of MTH1. To understand the relationship between protonation states and substrate binding, we determined the crystal structures of MTH1 at pH 7.7-9.7. With increasing pH, MTH1 gradually loses its substrate-binding ability, indicating that Asp119 is deprotonated at pH 8.0-9.1 in 8-oxo-dGTP recognition and Asp120 is deprotonated at pH 8.6-9.7 in 2-oxo-dATP recognition. These results confirm that MTH1 recognizes 8-oxo-dGTP and 2-oxo-dATP by exchanging the protonation state between Asp119 and Asp120 with higher pK .

PubMed: 36914375
DOI: 10.1002/1873-3468.14611

Experimental method

X-RAY DIFFRACTION (1.2 Å)