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Neutron diffraction reveals protonation states in pyridoxal‐5′‐phosphate‐free and glycine external aldimine‐bound serine hydroxymethyltransferase

Journal Article · · Federation of European Biochemical Societies (FEBS) Journal
DOI:https://doi.org/10.1111/febs.70260· OSTI ID:3018167
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. In conclusion, 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.
Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC05-00OR22725
Other Award/Contract Number:
R01GM137008
OSTI ID:
3018167
Journal Information:
Federation of European Biochemical Societies (FEBS) Journal, Journal Name: Federation of European Biochemical Societies (FEBS) Journal Journal Issue: 2 Vol. 293; ISSN 1742-464X; ISSN 1742-4658
Publisher:
Federation of European Biochemical SocietiesCopyright Statement
Country of Publication:
United States
Language:
English

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