Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) from Salmonella typhimurium complexed with arginine

Experimental Data Snapshot

  • Resolution: 1.86 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.176 

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The interplay of protein-ligand and water-mediated interactions shape affinity and selectivity in the LAO binding protein.

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.

(2020) FEBS J 287: 763-782

  • DOI: https://doi.org/10.1111/febs.15019
  • Primary Citation of Related Structures:  
    6MKU, 6MKW, 6MKX, 6ML0, 6ML9, 6MLA, 6MLD, 6MLE, 6MLG, 6MLI, 6MLJ, 6MLN, 6MLO, 6MLP, 6MLV

  • 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.

  • Organizational Affiliation

    Laboratorio de Química de Biomacromoléculas 3, Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine/arginine/ornithine-binding periplasmic proteinA [auth E]238Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
Gene Names: argTSTM2355
Find proteins for P02911 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P02911 
Go to UniProtKB:  P02911
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02911
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
ARG Binding MOAD:  6MLE Kd: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.86 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.318α = 90
b = 58.931β = 90
c = 115.383γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other governmentMexicoIN208418
Other governmentMexico221169
Other governmentMexico254514
Other governmentMexicoIN220516

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description