10YN

Joint X-ray/neutron structure of E53Q mutant of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT)

10YN の概要

• エントリーDOI: 10.2210/pdb10yn/pdb
• 分子名称: Serine hydroxymethyltransferase, SULFATE ION (3 entities in total)
• 機能のキーワード: homodimer, pyridoxal-5'-phosphate, one-carbon metabolism, inactive mutant, transferase
• 由来する生物種: Thermus thermophilus
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 89546.19

構造登録者

Kovalevsky, A.,Drago, V.N.,Phillips, R.S. (登録日: 2026-02-12, 公開日: 2026-05-20, 最終更新日: 2026-06-10)

主引用文献

Drago, V.N.,Phillips, R.S.,Kovalevsky, A.
Mutation of active site glutamate in serine hydroxymethyltransferase allows trapping a reactive intermediate: a combined neutron and X-ray crystallography study.
Rsc Adv, 16:22600-22609, 2026

PubMed Abstract: Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5'-phosphate (PLP) dependent enzyme that catalyzes a chemical transformation essential for the one-carbon (1C) metabolism. SHMT reversibly converts l-Ser into Gly and transfers a 1C unit to tetrahydrofolate (THF) to give 5,10-methylene-THF (5,10-MTHF). 5,10-MTHF, a 1C-unit donor, plays a crucial role in the downstream biomolecular syntheses required for the cell homeostasis and proliferation. SHMT is a prominent target for the drug discovery to battle bacterial and parasitic infections, and to treat various types of cancer. SHMT-catalyzed chemistry is governed by the general acid-base catalysis. Knowledge of the catalytic mechanism can aid drug design but can only be achieved when the atomic details of each reaction step are mapped, including accurate determination of hydrogen atom positions. Here we utilized the inactive E53Q mutant of () SHMT to directly determine protonation states with room-temperature neutron crystallography and to capture a reactive intermediate containing the PLP-l-Ser external aldimine and THF in the enzyme active site. We observed protonation of the Schiff base nitrogen (N) in the PLP internal aldimine but no change in the protonation states of other ionizable PLP groups and active site residues compared to wild-type SHMT. X-ray structural analysis of the ternary intermediate complex E53Q-Ser-THF that eluded previous structural characterization shows the strategic positioning of the E53Q side chain in close proximity to the external aldimine and THF and reinforces the proposed role for E53 as the driver of proton transfer events along the reaction pathway.

PubMed: 42112277
DOI: 10.1039/d6ra01814a

実験手法

NEUTRON DIFFRACTION (2.4 Å)
X-RAY DIFFRACTION (1.65 Å)