7NDW

ThyX-FADH2 soaked with 20 mM Formaldehyde

Summary for 7NDW

• Entry DOI: 10.2210/pdb7ndw/pdb
• Descriptor: Flavin-dependent thymidylate synthase, [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate, DI(HYDROXYETHYL)ETHER, ... (7 entities in total)
• Functional Keywords: flavin-dependent thymidylate synthase, methylenetetrahydrofolate, transferase
• Biological source: Thermotoga maritima
• Total number of polymer chains: 4
• Total formula weight: 114442.98

Authors

Bou-Nader, C.,Pecqueur, L.,Hamdane, D. (deposition date: 2021-02-02, release date: 2021-07-21, Last modification date: 2024-01-31)

Primary citation

Bou-Nader, C.,Stull, F.W.,Pecqueur, L.,Simon, P.,Guerineau, V.,Royant, A.,Fontecave, M.,Lombard, M.,Palfey, B.A.,Hamdane, D.
An enzymatic activation of formaldehyde for nucleotide methylation.
Nat Commun, 12:4542-4542, 2021

PubMed Abstract: Folate enzyme cofactors and their derivatives have the unique ability to provide a single carbon unit at different oxidation levels for the de novo synthesis of amino-acids, purines, or thymidylate, an essential DNA nucleotide. How these cofactors mediate methylene transfer is not fully settled yet, particularly with regard to how the methylene is transferred to the methylene acceptor. Here, we uncovered that the bacterial thymidylate synthase ThyX, which relies on both folate and flavin for activity, can also use a formaldehyde-shunt to directly synthesize thymidylate. Combining biochemical, spectroscopic and anaerobic crystallographic analyses, we showed that formaldehyde reacts with the reduced flavin coenzyme to form a carbinolamine intermediate used by ThyX for dUMP methylation. The crystallographic structure of this intermediate reveals how ThyX activates formaldehyde and uses it, with the assistance of active site residues, to methylate dUMP. Our results reveal that carbinolamine species promote methylene transfer and suggest that the use of a CHO-shunt may be relevant in several other important folate-dependent reactions.

PubMed: 34315871
DOI: 10.1038/s41467-021-24756-8

Experimental method

X-RAY DIFFRACTION (2 Å)