4NFX

Structure and atypical hydrolysis mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

Summary for 4NFX

• Entry DOI: 10.2210/pdb4nfx/pdb
• Related: 4nfw
• Descriptor: Putative Nudix hydrolase ymfB (2 entities in total)
• Functional Keywords: nudix hydrolase; ymfb; nucleoside triphosphatase; metal ions-based catalysis, nudix motif, phosphatase, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 8
• Total formula weight: 139606.83

Authors

Hong, M.K.,Kim, J.K.,Kang, L.W. (deposition date: 2013-11-01, release date: 2014-05-14, Last modification date: 2024-03-20)

Primary citation

Hong, M.K.,Ribeiro, A.J.M.,Kim, J.K.,Ngo, H.P.T.,Kim, J.,Lee, C.H.,Ahn, Y.J.,Fernandes, P.A.,Li, Q.,Ramos, M.J.,Kang, L.W.
Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli
Acta Crystallogr.,Sect.D, 70:1297-1310, 2014

PubMed Abstract: YmfB 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.

PubMed: 24816099
DOI: 10.1107/S1399004714002570

Experimental method

X-RAY DIFFRACTION (2.69 Å)