6MLV

Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) Y14A mutant from Salmonella typhimurium

6MLV の概要

• エントリーDOI: 10.2210/pdb6mlv/pdb
• 関連するPDBエントリー: 6MKU 6ML0 6ML9 6MLA 6MLD 6MLE 6MLG 6MLI 6MLJ 6MLN 6MLO 6MLP
• 分子名称: Lysine/arginine/ornithine-binding periplasmic protein (2 entities in total)
• 機能のキーワード: periplasmic binding protein, lao, thermodynamics, protein ligand complex, protein binding
• 由来する生物種: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 25966.22

構造登録者

Romero-Romero, S.,Vergara, R.,Espinoza-Perez, G.,Rodriguez-Romero, A. (登録日: 2018-09-28, 公開日: 2019-08-07, 最終更新日: 2024-10-16)

主引用文献

Vergara, R.,Romero-Romero, S.,Velazquez-Lopez, I.,Espinoza-Perez, G.,Rodriguez-Hernandez, A.,Pulido, N.O.,Sosa-Peinado, A.,Rodriguez-Romero, A.,Fernandez-Velasco, D.A.
The interplay of protein-ligand and water-mediated interactions shape affinity and selectivity in the LAO binding protein.
Febs J., 287:763-782, 2020

PubMed Abstract: The study of binding thermodynamics is essential to understand how affinity and selectivity are acquired in molecular complexes. Periplasmic binding proteins (PBPs) are macromolecules of biotechnological interest that bind a broad number of ligands and have been used to design biosensors. The lysine-arginine-ornithine binding protein (LAO) is a PBP of 238 residues that binds the basic amino acids l-arginine and l-histidine with nm and μm affinity, respectively. It has been shown that the affinity difference for arginine and histidine binding is caused by enthalpy, this correlates with the higher number of protein-ligand contacts formed with arginine. In order to elucidate the structural bases that determine binding affinity and selectivity in LAO, the contribution of protein-ligand contacts to binding energetics was assessed. To this end, an alanine scanning of the LAO-binding site residues was performed and arginine and histidine binding were characterized by isothermal titration calorimetry and X-ray crystallography. Although unexpected enthalpy and entropy changes were observed in some mutants, thermodynamic data correlated with structural information, especially, the binding heat capacity change. We found that selectivity is conferred by several residues rather than exclusive arginine-protein interactions. Furthermore, crystallographic structures revealed that protein-ligand contributions to binding thermodynamics are highly influenced by the solvent. Finally, we found a similar backbone conformation in all the closed structures obtained, but different structures in the open state, suggesting that the binding site residues of LAO play an important role in stabilizing not only the holo conformation, but also the apo state. DATABASE: Structural data are available in the Protein Data Bank database under the accession numbers 6MLE, 6MLN, 6MLG, 6MKX, 6MLI, 6MLA, 6MKU, 6MKW, 6ML0, 6MLD, 6MLV, 6MLO, 6MLP, 6ML9, 6MLJ.

PubMed: 31348608
DOI: 10.1111/febs.15019

実験手法

X-RAY DIFFRACTION (2.082 Å)