8SSJ

Room-temperature X-ray structure of human mitochondrial serine hydroxymethyltransferase (hSHMT2)

8SSJ の概要

• エントリーDOI: 10.2210/pdb8ssj/pdb
• 分子名称: Serine hydroxymethyltransferase, mitochondrial, CHLORIDE ION (3 entities in total)
• 機能のキーワード: pyridoxal 5'-phosphate, plp, fold type 1, one carbon metabolism, transferase
• 由来する生物種: Homo sapiens (human)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 104357.23

構造登録者

Drago, V.N.,Kovalevsky, A. (登録日: 2023-05-08, 公開日: 2023-08-16, 最終更新日: 2023-11-15)

主引用文献

Drago, V.N.,Campos, C.,Hooper, M.,Collins, A.,Gerlits, O.,Weiss, K.L.,Blakeley, M.P.,Phillips, R.S.,Kovalevsky, A.
Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography.
Commun Chem, 6:162-162, 2023

PubMed Abstract: Pyridoxal 5'-phosphate (PLP)-dependent enzymes utilize a vitamin B-derived cofactor to perform a myriad of chemical transformations on amino acids and other small molecules. Some PLP-dependent enzymes, such as serine hydroxymethyltransferase (SHMT), are promising drug targets for the design of small-molecule antimicrobials and anticancer therapeutics, while others have been used to synthesize pharmaceutical building blocks. Understanding PLP-dependent catalysis and the reaction specificity is crucial to advance structure-assisted drug design and enzyme engineering. Here we report the direct determination of the protonation states in the active site of Thermus thermophilus SHMT (TthSHMT) in the internal aldimine state using room-temperature joint X-ray/neutron crystallography. Conserved active site architecture of the model enzyme TthSHMT and of human mitochondrial SHMT (hSHMT2) were compared by obtaining a room-temperature X-ray structure of hSHMT2, suggesting identical protonation states in the human enzyme. The amino acid substrate serine pathway through the TthSHMT active site cavity was tracked, revealing the peripheral and cationic binding sites that correspond to the pre-Michaelis and pseudo-Michaelis complexes, respectively. At the peripheral binding site, the substrate is bound in the zwitterionic form. By analyzing the observed protonation states, Glu53, but not His residues, is proposed as the general base catalyst, orchestrating the retro-aldol transformation of L-serine into glycine.

PubMed: 37532884
DOI: 10.1038/s42004-023-00964-9

実験手法

X-RAY DIFFRACTION (2.5 Å)