Structural highlights
Publication Abstract from PubMedYmfB from Escherichia coli is the Nudix hydrolase involved in the metabolism of thiamine pyrophosphate, an important compound in primary metabolism and a cofactor of many enzymes. In addition, it hydrolyzes (d)NTPs to (d)NMPs and inorganic orthophosphates in a stepwise manner. The structures of YmfB alone and in complex with three sulfates and two manganese ions determined by X-ray crystallography, when compared with the structures of other Nudix hydrolases such as MutT, Ap4Aase and DR1025, provide insight into the unique hydrolysis mechanism of YmfB. Mass-spectrometric analysis confirmed that water attacks the terminal phosphates of GTP and GDP sequentially. Kinetic analysis of binding-site mutants showed that no individual residue is absolutely required for catalytic activity, suggesting that protein residues do not participate in the deprotonation of the attacking water. Thermodynamic integration calculations show that a hydroxyl ion bound to two divalent metal ions attacks the phosphate directly without the help of a nearby catalytic base. Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli.,Hong MK, Ribeiro AJ, Kim JK, Ngo HP, Kim J, Lee CH, Ahn YJ, Fernandes PA, Li Q, Ramos MJ, Kang LW Acta Crystallogr D Biol Crystallogr. 2014 May;70(Pt 5):1297-310. doi:, 10.1107/S1399004714002570. Epub 2014 Apr 29. PMID:24816099[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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