Crystallization and Preliminary X-ray Analysis of the Periplasmic Dipeptide Binding Protein from Escherichia coli

Hijacking of a Substrate-binding Protein Scaffold for use in Mycobacterial Cell Wall Biosynthesis

“…DppA from Escherichia coli), some members can bind ions, such as the nickel-binding protein, NikA. [47][48][49][50][51] The rmsd for the pairwise superpositions between LpqW and OppA, AppA, DppA and NikA (PDB codes 1jev, 1xoc, 1dpe and 1uiu, respectively) were 4.2 Å over 455 residues (Z-score 35.5); 4.1 Å over 394 residues (Z-score 23.2); 7.3 Å over 438 residues (Z-score 20.8); and 5.5 Å over 439 residues (Z-score 23.5), respectively, calculated over the entire LpqW monomer, using the program LSQMAN. 52 In some instances, these global comparative statistics improved considerably if one only superposed the individual domains.…”

The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands

“…This has led to the suggestion of a role for one or more of these residues in binding the carboxyl group of a dipeptide ligand. DppA has been crystallized in the presence of several dipeptides [30] and the structure has recently been solved (P Dunten and S Mowbray, Protein Sci., in press), revealing that in fact Arg355 is responsible for binding to the ligand C terminus (S Mowbray, personal communication).…”

Evaluation of the relative stability of liganded versus ligand‐free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method

“…The existence of open and closed conformations for bPBPs has been demonstrated by X‐ray crystallography for several proteins, including arabinose‐binding protein (ABP),6 leucine/isoleucine/valine‐binding protein (LIVBP),7 leucine‐binding protein (LBP),8 histidine‐binding protein (HBP),9, 10 molybdate‐binding protein (ModA),11 sulfate‐binding protein (SBP),12, 13 phosphate‐binding protein (PBP),14–16 galactose/glucose‐binding protein (GGBP),17–20 ribose‐binding protein (RBP),21–24 glutamine‐binding protein (GlnBP),25–27 lysine/arginine/ornithine‐binding protein (LAOBP),28, 29 allose‐binding protein (ALBP),30, 31 Haemophilus influenzae Fe 3+ ‐binding protein (hFBP),32, 33 vitamin B‐12‐binding protein (BtuF),34 Treponema pallidum Zn 2+ ‐binding protein (TroA),35, 36 dipeptide‐binding protein (DppA),37–39 oligopeptide‐binding protein (OppA),40–45 and maltose‐binding protein (MBP) 46–51. In addition, small‐angle X‐ray scattering (SAXS) experiments for ABP,52 RBP, MBP and GGBP53 have shown that the radius of gyration for these proteins decreases upon ligand binding, which is consistent with a change in overall protein conformation.…”