Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein with bound ligand isoleucine

Experimental Data Snapshot

  • Resolution: 1.96 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.183 

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Ligand-free and -bound structures of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport system: trajectory and dynamics of the interdomain rotation and ligand specificity.

Trakhanov, S.D.Vyas, N.K.Luecke, H.Kristensen, D.M.Ma, J.Quiocho, F.A.

(2005) Biochemistry 44: 6597-6608

  • DOI: https://doi.org/10.1021/bi047302o
  • Primary Citation of Related Structures:  
    1Z15, 1Z16, 1Z17, 1Z18

  • PubMed Abstract: 

    The leucine/isoleucine/valine-binding protein (LIVBP or LivJ) serves as the primary high-affinity receptor of the Escherichia coli ABC-type transporter for the three aliphatic amino acids. The first structure of LIVBP determined previously without bound ligand showed a molecule comprised of two domains which are far apart and bisected by a wide open, solvent-accessible cleft. Here we report the crystal structures of another ligand-free state and three complexes with the aliphatic amino acids. In the present ligand-free structure, the two domains are farther apart. In the three very similar complex structures, the two domains are in close proximity, and each desolvated ligand is completely engulfed in the cleft and bound by both domains. The two different ligand-free structures, combined with those of the very similar ligand-bound structures, indicate the trajectory and backbone torsion angle changes of the hinges that accompany domain closure and play crucial functional roles. The amino acids are bound by polar and nonpolar interactions, occurring predominantly in one domain. Consistent with the protein specificity, the aliphatic side chains of the ligands lie in a hydrophobic pocket fully formed following domain or cleft closure. Comparison of the structures of LIVBP with several different binding proteins indicates no correlations between the magnitudes of the hinge-bending angles and the protein masses, the ligand sizes, or the number of segments connecting the two domains. Results of normal-mode analysis and molecular dynamics simulations are consistent with the trajectory and intrinsic flexibility of the interdomain hinges and the dominance of one domain in ligand binding in the open state.

  • Organizational Affiliation

    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leu/Ile/Val-binding protein344Escherichia coli K-12Mutation(s): 0 
Gene Names: livJb3460JW3425
Find proteins for P0AD96 (Escherichia coli (strain K12))
Explore P0AD96 
Go to UniProtKB:  P0AD96
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AD96
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ILE

Download Ideal Coordinates CCD File 
C6 H13 N O2
Query on MRD

Download Ideal Coordinates CCD File 
C6 H14 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
ILE Binding MOAD:  1Z17 Kd: 900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.96 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.183 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.13α = 90
b = 99.13β = 90
c = 93.18γ = 120
Software Package:
Software NamePurpose
MACSCIENCEdata reduction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description