9O5G

Room-temperature joint X-ray/Neutron structure of Thermus thermophilus SHMT in complex with PLP-Gly external aldimine and 5-methyl-tetrahydrofolate (5MTHF)

9O5G の概要

• エントリーDOI: 10.2210/pdb9o5g/pdb
• 関連するPDBエントリー: 9O50
• 分子名称: Serine hydroxymethyltransferase, SULFATE ION, N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE], ... (5 entities in total)
• 機能のキーワード: plp-dependent enzyme, glycine external aldimine, 5-methyl-tetrahydrofolate, 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: 90145.78

構造登録者

Kovalevsky, A.,Drago, V.N.,Phillips, R.S. (登録日: 2025-04-10, 公開日: 2026-02-04)

主引用文献

Drago, V.N.,Blakeley, M.P.,Phillips, R.S.,Kovalevsky, A.
Neutron diffraction reveals protonation states in pyridoxal-5'-phosphate-free and glycine external aldimine-bound serine hydroxymethyltransferase.
Febs J., 293:582-597, 2026

PubMed Abstract: Serine hydroxymethyltransferase (SHMT) is a critical enzyme in the one-carbon (1C) metabolism pathway catalyzing the reversible conversion of L-Ser into Gly and concurrent transfer of 1C unit to tetrahydrofolate (THF) to give 5,10-methylene-THF (5,10-MTHF), which is used in the downstream syntheses of biomolecules critical for cell proliferation. The cellular 1C metabolism is hijacked by many cancer types to support cancer cell proliferation, making SHMT a promising target for the design and development of novel small-molecule antimetabolite chemotherapies. To advance structure-assisted drug design, knowledge of SHMT catalysis is crucial, but can only be fully realized when the atomic details of each reaction step governed by the acid-base catalysis are elucidated by visualizing active site hydrogen atoms. Here, we used room-temperature neutron crystallography to directly determine protonation states in Thermus thermophilus SHMT (TthSHMT), capturing protomer A in the apo form lacking the coenzyme pyridoxal 5'-phosphate (PLP), and protomer B as a ternary complex with PLP-Gly-external aldimine and (6S)-5-methyltetrahydrofolate (5MTHF). We observed protonation of the Schiff base nitrogen in PLP-Gly and neutrality of the catalytic Lys226 side chain in the ternary complex, whereas Lys226 is protonated and positively charged in the apo-active site. Furthermore, we obtained an X-ray structure of TthSHMT in complex with the substrate THF, which binds identically as 5MTHF at the peripheral binding site. The unique structural and functional information provided by neutron crystallography, in combination with X-ray structures, can be employed in the rational design of SHMT inhibitors.

PubMed: 40915980
DOI: 10.1111/febs.70260

実験手法

NEUTRON DIFFRACTION (2.1 Å)
X-RAY DIFFRACTION (1.7 Å)