6ML9

Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) D30A mutant from Salmonella typhimurium complexed with arginine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.687 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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.

(2019) Febs J. --: --

  • DOI: 10.1111/febs.15019
  • Primary Citation of Related Structures:  

  • 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 a ...

    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 (ITC) 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. This article is protected by copyright. All rights reserved.


    Organizational Affiliation

    Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México.,Laboratorio de Química de Biomacromoléculas 3, Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine/arginine/ornithine-binding periplasmic protein
E
238Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 1 
Gene Names: argT
Find proteins for P02911 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P02911
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
E
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ARG
Query on ARG

Download SDF File 
Download CCD File 
E
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.687 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.135 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.179α = 90.00
b = 57.766β = 90.00
c = 101.444γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXrefinement
PHENIXphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentMexicoIN208418
Other governmentMexico221169
Other governmentMexico254514
Other governmentMexicoIN220516

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release