6NNR

high-resolution structure of wild-type E. coli thymidylate synthase

「4KNZ」から置き換えられました 「2G8O」から置き換えられました 「4IW5」から置き換えられました

6NNR の概要

• エントリーDOI: 10.2210/pdb6nnr/pdb
• 分子名称: Thymidylate synthase, 2'-deoxy-5'-uridylic acid, 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID, ... (6 entities in total)
• 機能のキーワード: nucleotide synthesis, hydride transfer, methyl transfer, cancer drug target, transferase
• 由来する生物種: Escherichia coli (strain K12)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 63194.27

構造登録者

Stroud, R.M.,Finer-Moore, J. (登録日: 2019-01-15, 公開日: 2019-01-30, 最終更新日: 2024-11-20)

主引用文献

Wang, Z.,Sapienza, P.J.,Abeysinghe, T.,Luzum, C.,Lee, A.L.,Finer-Moore, J.S.,Stroud, R.M.,Kohen, A.
Mg2+ binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site.
J. Am. Chem. Soc., 135:7583-7592, 2013

PubMed Abstract: Thymidylate synthase (TSase) produces the sole intracellular de novo source of thymidine (i.e., the DNA base T) and thus is a common target for antibiotic and anticancer drugs. Mg(2+) has been reported to affect TSase activity, but the mechanism of this interaction has not been investigated. Here we show that Mg(2+) binds to the surface of Escherichia coli TSase and affects the kinetics of hydride transfer at the interior active site (16 Å away). Examination of the crystal structures identifies a Mg(2+) near the glutamyl moiety of the folate cofactor, providing the first structural evidence for Mg(2+) binding to TSase. The kinetics and NMR relaxation experiments suggest that the weak binding of Mg(2+) to the protein surface stabilizes the closed conformation of the ternary enzyme complex and reduces the entropy of activation on the hydride transfer step. Mg(2+) accelerates the hydride transfer by ~7-fold but does not affect the magnitude or temperature dependence of the intrinsic kinetic isotope effect. These results suggest that Mg(2+) facilitates the protein motions that bring the hydride donor and acceptor together, but it does not change the tunneling ready state of the hydride transfer. These findings highlight how variations in cellular Mg(2+) concentration can modulate enzyme activity through long-range interactions in the protein, rather than binding at the active site. The interaction of Mg(2+) with the glutamyl tail of the folate cofactor and nonconserved residues of bacterial TSase may assist in designing antifolates with polyglutamyl substitutes as species-specific antibiotic drugs.

PubMed: 23611499
DOI: 10.1021/ja400761x

実験手法

X-RAY DIFFRACTION (1.05 Å)