PDBsum entry 1xoc

Transport protein

PDB id: 1xoc

Contents

Protein chain

504 a.a.

Ligands

VAL-ASP-SER-LYS-ASN-THR-SER-SER-TRP

Metals

_ZN ×15

Waters ×441

References listed in PDB file

Key reference

Title

The structure of the oligopeptide-Binding protein, Appa, From bacillus subtilis in complex with a nonapeptide.

Authors

V.M.Levdikov, E.V.Blagova, J.A.Brannigan, L.Wright, A.A.Vagin, A.J.Wilkinson.

Ref.

J Mol Biol, 2005, 345, 879-892. [DOI no: 10.1016/j.jmb.2004.10.089]

PubMed id

15588833

Abstract

Besides their role as a source of amino acids for Bacillus subtilis, exogenous peptides play important roles in the signalling pathways leading to the development of competence and sporulation. B.subtilis has three peptide transport systems all belonging to the ATP-binding cassette family, a dipeptide permease (Dpp) and two oligopeptide permeases (Opp and App) with overlapping specificity. These comprise a membrane-spanning channel through which the peptide passes, a pair of ATPases which couple ATP hydrolysis to peptide translocation and a lipid-modified, membrane-anchored extracellular "binding-protein" that serves as the receptor for the system. Here, we present the crystal structure of a soluble form of the peptide-binding protein AppA, which has been solved to 1.6 A spacing by anomalous scattering and molecular replacement methods. The structure reveals a protein made of two distinct lobes with a topology similar to those of DppA from Escherichia coli and OppA from Salmonella typhimurium. Examination of the interlobe region reveals an enlarged pocket, containing electron density defining a nonapeptide ligand. The main-chain of the peptide is well defined and makes a series of polar contacts with the protein including salt-bridges at both its termini. The side-chain density is ambiguous in places, consistent with the interpretation that a population of peptides is bound, whose average electron density resembles the amino acid sequence N-VDSKNTSSW-C.

Figure 2.
Figure 2. Ribbon diagrams of the AppA structure. A, The tri-domain organisation; domains I and II are coloured in dark and light blue, respectively, domain III is coloured in green. The amino (N) and carboxyl (C) termini are labelled. The peptide is coloured in red. B, The course of the polypeptide chain, colour-ramped from its N terminus (blue) to its C terminus (red) with the peptide ligand shown in space-filling format. This and a number of subsequent illustrations were produced in MOLSCRIPT59 and rendered with the program Raster3D.60

Figure 3.
Figure 3. Structure and interactions of the nonapeptide ligand in AppA. A, Electron density associated with the peptide ligand in the binding pocket of AppA together with the modelled nonapeptide. The map is calculated with coefficients 2F[obs]-F[calc] and a[calc], and the electron density displayed is contoured at 0.8 standard deviation from the mean density of the map. The ligand atoms are coloured according to atom type with carbon in grey, oxygen in red and nitrogen in blue. The amino (N) and carboxyl (C) termini are labelled. B, Stereo cross-section of the AppA structure illustrating the nonapeptide ligand and some of its surrounding residues in AppA. The ligand is coloured green and protein atoms are coloured according to atom type as described above and with sulphur in yellow. Water molecules are represented by red spheres. C, The extended set of interactions formed by Arg373 of AppA and the main chain of the peptide. Residues 5-9 of the peptide are shown with charge-charge/dipole interactions indicated by the dotted lines.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 345, 879-892) copyright 2005.

Secondary reference #1

Title

Crystallization of the oligopeptide-Binding protein appa from bacillus subtilis.

Authors

L.Wright, E.Blagova, V.M.Levdikov, J.A.Brannigan, R.J.Pattenden, J.Chambers, A.J.Wilkinson.

Ref.

Acta Crystallogr D Biol Crystallogr, 2004, 60, 175-177.

PubMed id

14684921