The crystal structure of glutamine-binding protein from Escherichia coli

The crystal structure of the glutamine-binding protein (GlnBP) from Escherichia coli in a ligand-free ''open'' conformational state has been determined by isomorphous replacement methods and refined to an R-value of 21.4% at 2.3 Angstrom resolution. There are two molecules in the asymmetric unit, related by pseudo 4-fold screw symmetry. The refined model consists of 3587 non-hydrogen atoms from 440 residues (two monomers), and 159 water molecules. The structure has root-mean-square deviations of 0.013 Angstrom from ''ideal'' bond lengths and 1.5 degrees from ''ideal'' bond angles. The GlnBP molecule has overall dimensions of approximately 60 Angstrom x 40 Angstrom x 35 Angstrom and is made up of two domains (termed large and small), which exhibit a similar supersecondary structure, linked by two antiparallel beta-strands. The small domain contains three alpha-helices and four parallel and one antiparallel beta-strands. The large domain is similar to the small domain but contains two additional alpha-helices and three more short antiparallel beta-strands. A comparison of the secondary structural motifs of GlnBP with those of other periplasmic binding proteins is discussed. A model of the ''closed form'' GlnBP-Gln complex has been proposed based on the crystal structures of the histidine-binding protein-His complex and ''open form'' GlnBP. This model has been successfully used as a search model in the crystal structure determination of the ''closed form'' GlnBP-Gln complex by molecular replacement methods. The model agrees remarkably well with the crystal structure of the Gln-GlnBP complex with root-mean-square deviation of 1.29 Angstrom. Our study shows that, at least in our case, it is possible to predict-one conformational state of a periplasmic binding protein from another conformational state of the protein. The glutamine-binding pockets of the model and the crystal structure are compared and the modeling technique is described. (C) 1996 Academic Press Limited