Crystallization and preliminary diffraction studies of Nudix hydrolase YmfB from Escherichia coli K-1.
Nudix hydrolases are a family of proteins that contains the Nudix signature of the characteristic amino-acid sequence Gx(5)Ex(5) [UA]xREx(2)EExGU, 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 C222(1) and the other a monoclinic space group P2(1), diffracted to 2.7 A and 2.6 A resolution, and had unit cell parameters of a = 68.7 A, b = 283.1 A, c = 70.4 A and a = 69.1 A, b = 70.3 A, c = 145.6 A, beta = 103.3 degrees , respectively. For the C222(1) space group, four or five monomers exist in the asymmetric unit, with a corresponding V(m) of 2.48 or 1.99 A(3) Da(-1) and a solvent content of 50.5 or 38.2%. For the P2(1) space group, eight or nine monomers exist in the asymmetric unit, with a corresponding V(m) of 2.49 or 2.21 A(3) Da(-1) and a solvent content of 50.7 or 44.5%.
Hong
Myoung-Ki
MK
Department of Advanced Technology Fusion, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea.
Kim
Jin-Kwang
JK
Ahn
Yeh-Jin
YJ
Kang
Lin-Woo
LW
D000595:Amino Acid Sequence; D003001:Cloning, Molecular; D003460:Crystallization; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D011755:Pyrophosphatases / Q000737:chemistry*; D016415:Sequence Alignment
D029968:Escherichia coli Proteins; D011755:Pyrophosphatases; C513850:YmfB protein, E coli