The crystal structure of glutamine-binding protein from Escherichia coli

Abstract

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 Å 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 Å from 'ideal' bond lengths and 1.5° from 'ideal' bond angles. The GlnBP molecule has overall dimensions of approximately 60 Å x 40 Å x 35 Å and is made up of two domains (termed large and small), which exhibit a similar supersecondary structure, linked by two antiparallel β-strands. The small domain contains three α-helices and four parallel and one antiparallel β-strands. The large domain is similar to the small domain but contains two additional α-helices and three more short antiparallel β-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 Å. 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.