4FZB

Structure of thymidylate synthase ThyX complexed to a new inhibitor

Summary for 4FZB

• Entry DOI: 10.2210/pdb4fzb/pdb
• Descriptor: Probable thymidylate synthase, FLAVIN-ADENINE DINUCLEOTIDE, 2-hydroxy-3-(4-methoxybenzyl)naphthalene-1,4-dione, ... (5 entities in total)
• Functional Keywords: homotetramer, fad-dependent thymidylate synthase, transferase-transferase inhibitor complex, transferase/transferase inhibitor
• Biological source: Paramecium bursaria Chlorella virus 1 (PBCV-1)
• Total number of polymer chains: 16
• Total formula weight: 437697.38

Authors

Basta, T.,Boum, Y.,Briffotaux, J.,Becker, H.F.,Lamarre-Jouenne, I.,Lambry, J.C.,Skouloubris, S.,Liebl, U.,van Tilbeurgh, H.,Graille, M.,Myllylkallio, H. (deposition date: 2012-07-06, release date: 2013-05-22, Last modification date: 2023-09-13)

Primary citation

Basta, T.,Boum, Y.,Briffotaux, J.,Becker, H.F.,Lamarre-Jouenne, I.,Lambry, J.C.,Skouloubris, S.,Liebl, U.,Graille, M.,van Tilbeurgh, H.,Myllykallio, H.
Mechanistic and structural basis for inhibition of thymidylate synthase ThyX.
Open Biology, 2:120120-120120, 2012

PubMed Abstract: Nature has established two mechanistically and structurally unrelated families of thymidylate synthases that produce de novo thymidylate or dTMP, an essential DNA precursor. Representatives of the alternative flavin-dependent thymidylate synthase family, ThyX, are found in a large number of microbial genomes, but are absent in humans. We have exploited the nucleotide binding pocket of ThyX proteins to identify non-substrate-based tight-binding ThyX inhibitors that inhibited growth of genetically modified Escherichia coli cells dependent on thyX in a manner mimicking a genetic knockout of thymidylate synthase. We also solved the crystal structure of a viral ThyX bound to 2-hydroxy-3-(4-methoxybenzyl)-1,4-naphthoquinone at a resolution of 2.6 Å. This inhibitor was found to bind within the conserved active site of the tetrameric ThyX enzyme, at the interface of two monomers, partially overlapping with the dUMP binding pocket. Our studies provide new chemical tools for investigating the ThyX reaction mechanism and establish a novel mechanistic and structural basis for inhibition of thymidylate synthesis. As essential ThyX proteins are found e.g. in Mycobacterium tuberculosis and Helicobacter pylori, our studies have also potential to pave the way towards the development of new anti-microbial compounds.

PubMed: 23155486
DOI: 10.1098/rsob.120120

Experimental method

X-RAY DIFFRACTION (2.59 Å)