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Crystallization and Preliminary Diffraction Studies of Nudix Hydrolase YmfB from Escherichia coli K-1

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Nudix hydrolases are a family of proteins that contains the Nudix signature of the characteristic amino-acid sequence Gx5Ex5[UA]xREx2EExGU, where x represents any amino acid and U usually a bulky hydrophobic amino acid, such as Leu, Val, or Ile. They ubiquitously exist in more than 200 species. YmfB, a novel Nudix hydrolase found in Escherichia coli, is a nonspecific nucleoside tri- and di-phosphatase, which atypically releases inorganic orthophosphate from triphosphates instead of pyrophosphate. In this study, YmfB was cloned, overexpressed, and crystallized. Two different crystals, one belonging to an orthorhombic space group C2221 and the other a monoclinic space group P21, diffracted to 2.7 Å and 2.6 Å resolution, and had unit cell parameters of a = 68.7 Å, b = 283.1 Å, c = 70.4 Å and a = 69.1 Å, b = 70.3 Å, c = 145.6 Å, β = 103.3°, respectively. For the C2221 space group, four or five monomers exist in the asymmetric unit, with a corresponding Vm of 2.48 or 1.99 Å3 Da-1 and a solvent content of 50.5 or 38.2%. For the P21 space group, eight or nine monomers exist in the asymmetric unit, with a corresponding Vm of 2.49 or 2.21 Å3 Da-1 and a solvent content of 50.7 or 44.5%.

Keywords: Nudix hydrolase; YmfB; crystallization; nucleoside triphosphatase

Document Type: Research Article


Publication date: January 1, 2009

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  • Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.

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