Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog
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Title
Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate AnalogAuthor (s)
Date
2021-04-08Publisher
American Chemical SocietyISSN
0006-2960; 1520-4995Bibliographic citation
Svetlana A. Kholodar, Janet S. Finer-Moore, Katarzyna Świderek, Kemel Arafet, Vicent Moliner, Robert M. Stroud, and Kohen, A. (2021) Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog. Biochemistry 2021 60 (16), 1243-1247, DOI: 10.1021/acs.biochem.1c00063Type
info:eu-repo/semantics/articlePublisher version
https://pubs.acs.org/doi/abs/10.1021/acs.biochem.1c00063Version
info:eu-repo/semantics/submittedVersionSubject
Abstract
Methylation of 2-deoxyuridine-5′-monophosphate (dUMP) at the C5 position by the obligate dimeric thymidylate synthase (TSase) in the sole de novo biosynthetic pathway to thymidine 5′-monophosphate (dTMP) proceeds by ... [+]
Methylation of 2-deoxyuridine-5′-monophosphate (dUMP) at the C5 position by the obligate dimeric thymidylate synthase (TSase) in the sole de novo biosynthetic pathway to thymidine 5′-monophosphate (dTMP) proceeds by forming a covalent ternary complex with dUMP and cosubstrate 5,10-methylenetetrahydrofolate. The crystal structure of an analog of this intermediate gives important mechanistic insights but does not explain the half-of-the-sites activity of the enzyme. Recent experiments showed that the C5 proton and the catalytic Cys are eliminated in a concerted manner from the covalent ternary complex to produce a noncovalent bisubstrate intermediate. Here, we report the crystal structure of TSase with a close synthetic analog of this intermediate in which it has partially reacted with the enzyme but in only one protomer, consistent with the half-of-the-sites activity of this enzyme. Quantum mechanics/molecular mechanics simulations confirmed that the analog could undergo catalysis. The crystal structure shows a new water 2.9 Å from the critical C5 of the dUMP moiety, which in conjunction with other residues in the network, may be the elusive general base that abstracts the C5 proton of dUMP during the reaction. [-]
Is part of
Biochemistry, 2021, vol. 60, no 16Funder Name
National Institutes of Health (NIH) | Ministerio de Ciencia, Innovación y Universidades | Generalitat Valenciana | Universitat Jaume I
Project code
R01 GM024485 | R01 GM65368 | PGC2018–094852–B–C21 | PID2019–107098RJ–I00 | AICO/2019/195 | SEJI/2020/007 | APOSTD/2020/015 | UJI–A2019–04 | UJI–B2020–03
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© The Royal Society of Chemistry
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