PDBsum entry 1olc

Complex (binding protein/peptide)

PDB id: 1olc

Contents

Protein chain

517 a.a. *

Ligands

LYS-LYS-LYS-ALA

IUM ×8

Waters ×337

* Residue conservation analysis

References listed in PDB file

Key reference

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

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 95%.

Abstract

BACKGROUND: The periplasmic oligopeptide-binding protein OppA has a remarkably broad substrate specificity, binding peptides of two or five amino-acid residues with high affinity, but little regard to sequence. It is therefore an ideal system for studying how different chemical groups can be accommodated in a protein interior. The ability of the protein to bind peptides of different lengths has been studied by co-crystallising it with different ligands. RESULTS: Crystals of OppA from Salmonella typhimurium complexed with the peptides Lys-Lys-Lys (KKK) and Lys-Lys-Lys-Ala (KKKA) have been grown in the presence of uranyl ions which form important crystal contacts. These structures have been refined to 1.4 A and 2.1 A, respectively. The ligands are completely enclosed, their side chains pointing into large hydrated cavities and making few strong interactions with the protein. CONCLUSIONS: Tight peptide binding by OppA arises from strong hydrogen bonding and electrostatic interactions between the protein and the main chain of the ligand. Different basic side chains on the protein form salt bridges with the C terminus of peptide ligands of different lengths.

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 reprinted by permission from Cell Press: Structure (1995, 3, 1395-1406) copyright 1995.

Secondary reference #1

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 #2

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