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

• Published in: Journal of molecular biology Vol. 280; no. 1; pp. 153 - 166
• Main Authors: Koellner, Gertraud, Luić, Marija, Shugar, David, Saenger, Wolfram, Bzowska, Agnieszka
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 03.07.1998
• Subjects: Animals; Binding Sites; Cattle; crystallization; Crystallography, X-Ray; E. coli formycin B; Escherichia coli - enzymology; Formycins - chemistry; Formycins - metabolism; Humans; Inosine; Mammals; Models, Molecular; Nucleosides - metabolism; Phosphates - metabolism; Protein Conformation; purine nucleoside phosphorylase; Purine-Nucleoside Phosphorylase - chemistry; Purine-Nucleoside Phosphorylase - metabolism; Substrate Specificity; Sulfates - metabolism; X-ray crystallography; X-ray crystallography; PNP; K i; E. coli formycin B; crystallization; purine nucleoside phosphorylase; K m; RMS; M r; TRIS; PDB
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1006/jmbi.1998.1799

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 122 with unit cell dimensions a = 123.11, c = 241.22 Å 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, England). The crystal structure was determined by molecular replacement and refined at 2.1 Å 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. In all monomers the nucleosides are in the high syn conformation about the glycosidic bonds with χ in the range 100 to 130°. The architecture of the active centre is in line with the known broad specificity and the kinetic properties of E. coli PNP.