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

• Tipo: Artigo em Revista Científica Internacional
• Data: 2014

Autores

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

Revista

Título: Acta Crystallographica Section D: Biological Crystallography

Vol. 70

Páginas: 1297-1310

ISSN: 0907-4449

Editora: Blackwell

Indexação

ISI Web of Knowledge - 6 Citações

Scopus - 6 Citações

Classificação Científica

FOS: Ciências exactas e naturais > Química

Outras Informações

ID Authenticus: 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.

Idioma: Inglês

Tipo (Avaliação Docente): Científica

Nº de páginas: 14