Crystal structure of the ternary complex of E-coli purine nucleoside phosphorylase with formycin B, a structural analogue of the substrate inosine, and phosphate (sulphate) at 2.1 Å resolution

被引:80
作者
Koellner, G
Luic, M
Shugar, D
Saenger, W
Bzowska, A
机构
[1] Univ Warsaw, Inst Expt Phys, Dept Biophys, PL-02089 Warsaw, Poland
[2] Rudjer Boskovic Inst, Zagreb 10000, Croatia
[3] Free Univ Berlin, Inst Kristallog, D-14195 Berlin, Germany
关键词
purine nucleoside phosphorylase; E-coli formycin B; crystallization; X-ray crystallography;
D O I
10.1006/jmbi.1998.1799
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The ternary complex of purine nucleoside phosphorylase from E. coli with formycin B and a sulphate or phosphate ion crystallized in the hexagonal space group P6(1)22 with unit cell dimensions a = 123.11, c = 241.22 Angstrom and three monomers per asymmetric unit. The biologically active hexamer is formed through 2-fold crystallographic symmetry, constituting a trimer of dimers. High-resolution X-ray diffraction data were collected using synchrotron radiation (Daresbury, En,oland). The crystal structure was determined by molecular replacement and refined at 2.1 Angstrom resolution to an R-value of 0.196. There is one active centre per monomer, composed of residues belonging to two subunits Of one dimer. The phosphate binding site is strongly positively charged and consists of three arginine residues (Arg24, Arg87 and Arg43 from a neighbouring subunit), Ser90 and Gly20. It is occupied by a sulphate or phosphate anion, each oxygen atom of which accepts at least two hydrogen bonds or salt-bridges. The sulphate or phosphate anion is also in direct contact with the ribose moiety of formycin B. The ribose binding site is composed of Ser90, Met180, Glu181 and His4, the latter belonging to the neighbouring subunit. The base binding site is exposed to solvent, and the base is unspecifically bound through a chain of water molecules and aromatic-aromatic interactions. Ln all monomers the nucleosides are in the high syn conformation about the glycosidic bonds with chi in the range 100 to 130 degrees. The architecture of the active centre is in line with the known broad specificity and the kinetic properties of E. coli PNP. (C) 1998 Academic Press.
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页码:153 / 166
页数:14
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