PDBsum entry 1b3f

Peptide binding protein

PDB id: 1b3f

Contents

Protein chain

517 a.a. *

Ligands

LYS-HIS-LYS

Metals

IUM ×8

Waters ×455

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystallographic and calorimetric analysis of peptide binding to oppa protein.

Authors

S.H.Sleigh, P.R.Seavers, A.J.Wilkinson, J.E.Ladbury, J.R.Tame.

Ref.

J Mol Biol, 1999, 291, 393-415. [DOI no: 10.1006/jmbi.1999.2929]

PubMed id

10438628

Abstract

Isothermal titration calorimetry has been used to study the binding of 20 different peptides to the peptide binding protein OppA, and the crystal structures of the ligand complexes have been refined. This periplasmic binding protein, part of the oligopeptide permease system of Gram negative bacteria, has evolved to bind and enclose small peptides of widely varying sequences. The peptides used in this study have the sequence Lys-X-Lys, where X is any of the 20 commonly occurring amino acids. The various side-chains found at position 2 on the ligand fit into a hydrated pocket. The majority of side-chains are restrained to particular conformations within the pocket. Water molecules act as flexible adapters, matching the hydrogen-bonding requirements of the protein and ligand and shielding charges on the buried ligand. This use of water by OppA to broaden the repertoire of its binding site is not unique, but contrasts sharply with other proteins which use water to help bind ligands highly selectively. Predicting the thermodynamics of binding from the structure of the complexes is highly complicated by the influence of water on the system.

Figure 2.
Figure 2. Bar chart showing the logarithm of KD (nM) for each of the ligands, in ascending order.

The above figure is reprinted by permission from Elsevier: J Mol Biol (1999, 291, 393-415) copyright 1999.

Secondary reference #1

Title

The role of water in sequence-Independent ligand binding by an oligopeptide transporter protein.

Authors

J.R.Tame, S.H.Sleigh, A.J.Wilkinson, J.E.Ladbury.

Ref.

Nat Struct Biol, 1996, 3, 998.

PubMed id

8946852

Secondary reference #2

Title

The crystal structures of the oligopeptide-Binding protein oppa complexed with tripeptide and tetrapeptide ligands.

Authors

J.R.Tame, E.J.Dodson, G.Murshudov, C.F.Higgins, A.J.Wilkinson.

Ref.

Structure, 1995, 3, 1395-1406. [DOI no: 10.1016/S0969-2126(01)00276-3]

PubMed id

8747465

Figure 1.
Figure 1. Stereo Cα trace of OppA in the closed, ligand bound form. The tri-lysine ligand is shown in thicker lines. Figure 1. Stereo Cα trace of OppA in the closed, ligand bound form. The tri-lysine ligand is shown in thicker lines.

Figure 5.
Figure 5. . Schematic diagram illustrating the interactions made by the main chain of the tri-lysine ligand with OppA. Protein residues are labelled. Hydrogen bonding and electrostatic interactions are indicated by the dotted lines. R1, R2 and R3 indicate the ligand side chains. Figure 5. . Schematic diagram illustrating the interactions made by the main chain of the tri-lysine ligand with OppA. Protein residues are labelled. Hydrogen bonding and electrostatic interactions are indicated by the dotted lines. R1, R2 and R3 indicate the ligand side chains.

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #3

Title

Structure determination of oppa at 2.3 a resolution using multiple-Wavelength anomalous dispersion methods.

Authors

I.D.Glover, R.C.Denny, N.D.Nguti, S.M.Mcsweeney, S.H.Kinder, A.W.Thompson, E.J.Dodson, A.J.Wilkinson, J.R.Tame.

Ref.

Acta Crystallogr D Biol Crystallogr, 1995, 51, 39-47. [DOI no: 10.1107/S090744499400692X]

PubMed id

15299334

Figure 2.
Fig. 2. Harker section, (w = 1/2), of the Patterson maps calculated with coefficients (a) anomalous differences recorded at a wavelength of 0.719 , corresponding to the white­line feature observed in XANES spectrum of OppA­L and (b) dispersive differences between data sets ,A~ and ,12. The Harker vectors corresponding to self vectors (+) and cross vectors ( ) resulting from the Patterson search procedue of SHELX90 are superimposed.

The above figure is reproduced from the cited reference with permission from the IUCr

Secondary reference #4

Title

The structural basis of sequence-Independent peptide binding by oppa protein.

Authors

J.R.Tame, G.N.Murshudov, E.J.Dodson, T.K.Neil, G.G.Dodson, C.F.Higgins, A.J.Wilkinson.

Ref.

Science, 1994, 264, 1578-1581. [DOI no: 10.1126/science.8202710]

PubMed id

8202710