5IOT

Flavin-dependent thymidylate synthase R174A variant in complex with FAD and dUMP

Summary for 5IOT

• Entry DOI: 10.2210/pdb5iot/pdb
• Related: 5ioq 5ior 5iot
• Descriptor: Thymidylate synthase ThyX, FLAVIN-ADENINE DINUCLEOTIDE, 2'-DEOXYURIDINE 5'-MONOPHOSPHATE, ... (4 entities in total)
• Functional Keywords: fad-dependent, nucleotide biosynthesis, reductive methylation, transferase
• Biological source: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
• Total number of polymer chains: 4
• Total formula weight: 114045.18

Authors

Bernard, S.M.,Stull, F.W.,Smith, J.L. (deposition date: 2016-03-08, release date: 2016-06-08, Last modification date: 2023-09-27)

Primary citation

Stull, F.W.,Bernard, S.M.,Sapra, A.,Smith, J.L.,Zuiderweg, E.R.,Palfey, B.A.
Deprotonations in the Reaction of Flavin-Dependent Thymidylate Synthase.
Biochemistry, 55:3261-3269, 2016

PubMed Abstract: Many microorganisms use flavin-dependent thymidylate synthase (FDTS) to synthesize the essential nucleotide 2'-deoxythymidine 5'-monophosphate (dTMP) from 2'-deoxyuridine 5'-monophosphate (dUMP), 5,10-methylenetetrahydrofolate (CH2THF), and NADPH. FDTSs have a structure that is unrelated to the thymidylate synthase used by humans and a very different mechanism. Here we report nuclear magnetic resonance evidence that FDTS ionizes N3 of dUMP using an active-site arginine. The ionized form of dUMP is largely responsible for the changes in the flavin absorbance spectrum of FDTS upon dUMP binding. dUMP analogues also suggest that the phosphate of dUMP acts as the base that removes the proton from C5 of the dUMP-methylene intermediate in the FDTS-catalyzed reaction. These findings establish additional differences between the mechanisms of FDTS and human thymidylate synthase.

PubMed: 27214228
DOI: 10.1021/acs.biochem.6b00510

Experimental method

X-RAY DIFFRACTION (2 Å)