1B5J

OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KQK

Summary for 1B5J

• Entry DOI: 10.2210/pdb1b5j/pdb
• Descriptor: PROTEIN (OLIGO-PEPTIDE BINDING PROTEIN), PROTEIN (LYS-GLN-LYS), URANIUM ATOM, ... (4 entities in total)
• Functional Keywords: complex (peptide transport-peptide), peptide transport, peptide binding protein
• Biological source: Salmonella typhimurium
• Total number of polymer chains: 2
• Total formula weight: 61187.72

Authors

Tame, J.R.H.,Wilkinson, A.J. (deposition date: 1999-01-06, release date: 1999-01-13, Last modification date: 2024-10-16)

Primary citation

Sleigh, S.H.,Seavers, P.R.,Wilkinson, A.J.,Ladbury, J.E.,Tame, J.R.
Crystallographic and calorimetric analysis of peptide binding to OppA protein.
J.Mol.Biol., 291:393-415, 1999

PubMed 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.

PubMed: 10438628
DOI: 10.1006/jmbi.1999.2929

Experimental method

X-RAY DIFFRACTION (1.8 Å)