Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

• Type: Article in International Scientific Journal
• Date: 2014

Authors

Myoung Ki Hong (Author) Other; Antonio J M Ribeiro (Author) Other; Jin Kwang Kim (Author) Other; Ngo, HPT (Author) Other; Jiyoung Kim (Author) Other; Choong Hwan Lee (Author) Other; Yeh Jin Ahn (Author) Other; Pedro Alexandrino Fernandes (Author) FCUP; Qing Li (Author) Other; Maria Joao Ramos (Author) FCUP; Lin Woo Kang (Author) Other

Journal

Title: Acta Crystallographica Section D: Biological Crystallography

Vol. 70

Pages: 1297-1310

ISSN: 0907-4449

Publisher: Blackwell

Indexing

ISI Web of Knowledge - 6 Citations

Scopus - 6 Citations

Scientific classification

FOS: Natural sciences > Chemical sciences

Other information

Authenticus ID: P-009-GG6

DOI: 10.1107/s1399004714002570

Abstract (EN): 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, Ap(4)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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 14