{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T01:48:30Z","timestamp":1776476910430,"version":"3.51.2"},"reference-count":47,"publisher":"International Union of Crystallography (IUCr)","issue":"5","license":[{"start":{"date-parts":[[2014,4,29]],"date-time":"2014-04-29T00:00:00Z","timestamp":1398729600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/journals.iucr.org\/services\/copyrightpolicy.html"},{"start":{"date-parts":[[2014,4,29]],"date-time":"2014-04-29T00:00:00Z","timestamp":1398729600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/journals.iucr.org\/services\/copyrightpolicy.html#TDM"}],"content-domain":{"domain":["iucr.org","wiley.com","iucrj.org"],"crossmark-restriction":true},"short-container-title":["Acta Crystallogr D Biol Crystallogr","Acta Crystallogr D","Acta Crystallogr D Biol Cryst","Acta Cryst D","Acta Cryst D Biol Crystallogr","Acta Cryst D Biol Cryst","Acta Cryst Sect D","Acta Cryst Sect D Biol Cryst","Acta Crystallogr Sect D","Acta Crystallogr Sect D Biol Crystallogr"],"published-print":{"date-parts":[[2014,5,1]]},"abstract":"<jats:p>YmfB from<jats:italic>Escherichia coli<\/jats:italic>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, Ap<jats:sub>4<\/jats:sub>Aase 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.<\/jats:p>","DOI":"10.1107\/s1399004714002570","type":"journal-article","created":{"date-parts":[[2014,4,30]],"date-time":"2014-04-30T17:52:14Z","timestamp":1398880334000},"page":"1297-1310","update-policy":"https:\/\/doi.org\/10.1107\/cm_01","source":"Crossref","is-referenced-by-count":6,"title":["Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from<i>Escherichia coli<\/i>"],"prefix":"10.1107","volume":"70","author":[{"given":"Myoung-Ki","family":"Hong","sequence":"first","affiliation":[]},{"given":"Ant\u00f3nio J. 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