1QKB

OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KVK

Summary for 1QKB

• Entry DOI: 10.2210/pdb1qkb/pdb
• Related: 1B05 1B0H 1B1H 1B2H 1B32 1B3F 1B3G 1B3H 1B3L 1B40 1B46 1B4H 1B4Z 1B51 1B52 1B58 1B5H 1B5I 1B5J 1B6H 1B7H 1B9J 1JET 1JEU 1JEV 1OLA 1OLC 1QKA 1RKM 2OLB 2RKM
• Descriptor: PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN, PEPTIDE LYS-VAL-LYS, URANYL (VI) ION, ... (5 entities in total)
• Functional Keywords: protein transport, complex (peptide transport-peptide), peptide transport
• Biological source: SALMONELLA TYPHIMURIUM; More
• Cellular location: Periplasm: P06202
• Total number of polymer chains: 2
• Total formula weight: 61828.02

Authors

Tame, J.R.H.,Sleigh, S.H.,Wilkinson, A.J. (deposition date: 1999-07-14, release date: 1999-09-09, Last modification date: 2024-10-23)

Primary citation

Sleigh, S.H.,Seavers, P.R.,Wilkinson, A.J.,Ladbury, J.E.,Tame, J.R.H.
Crystallographic and Calorimetric Analysis of Peptide Binding to Oppa Protein
J.Mol.Biol., 291:393-, 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)