2QO5

Crystal structure of the cysteine 91 threonine mutant of zebrafish liver bile acid-binding protein complexed with cholic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

A Single Amino Acid Mutation in Zebrafish (Danio rerio) Liver Bile Acid-binding Protein Can Change the Stoichiometry of Ligand Binding.

Capaldi, S.Guariento, M.Saccomani, G.Fessas, D.Perduca, M.Monaco, H.L.

(2007) J Biol Chem 282: 31008-31018

  • DOI: https://doi.org/10.1074/jbc.M705399200
  • Primary Citation of Related Structures:  
    2QO4, 2QO5, 2QO6

  • PubMed Abstract: 

    In all of the liver bile acid-binding proteins (L-BABPs) studied so far, it has been found that the stoichiometry of binding is of two cholate molecules per internal binding site. In this paper, we describe the expression, purification, crystallization, and three-dimensional structure determination of zebrafish (Danio rerio) L-BABP to 1.5A resolution, which is currently the highest available for a protein of this family. Since we have found that in zebrafish, the stoichiometry of binding in the protein cavity is of only one cholate molecule per wild type L-BABP, we examined the role of two crucial amino acids present in the binding site. Using site-directed mutagenesis, we have prepared, crystallized, and determined the three-dimensional structure of co-crystals of two mutants. The mutant G55R has the same stoichiometry of binding as the wild type protein, whereas the C91T mutant changes the stoichiometry of binding from one to two ligand molecules in the cavity and therefore appears to be more similar to the other members of the L-BABP family. Based on the presence or absence of a single disulfide bridge, it can be postulated that fish should bind a single cholate molecule, whereas amphibians and higher vertebrates should bind two. Isothermal titration calorimetry has also revealed the presence in the wild type protein and the G55R mutant of an additional binding site, different from the first and probably located on the surface of the molecule.


  • Organizational Affiliation

    Biocrystallography Laboratory, Department of Science and Technology, University of Verona, Ca Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Liver-basic fatty acid binding protein129Danio rerioMutation(s): 1 
Gene Names: fabp10
UniProt
Find proteins for Q9I8L5 (Danio rerio)
Explore Q9I8L5 
Go to UniProtKB:  Q9I8L5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I8L5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.012α = 90
b = 63.276β = 105.51
c = 35.671γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description