2MM3

Solution NMR structure of the ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural determinants of ligand binding in the ternary complex of human ileal bile acid binding protein with glycocholate and glycochenodeoxycholate obtained from solution NMR

Horvath, G.Bencsura, A.Simon, A.Tochtrop, G.P.DeKoster, G.T.Covey, D.F.Cistola, D.P.Toke, O.

(2016) FEBS J. 283: 541-555

  • DOI: 10.1111/febs.13610

  • PubMed Abstract: 
  • Besides aiding digestion, bile salts are important signal molecules exhibiting a regulatory role in metabolic processes. Human ileal bile acid binding protein (I-BABP) is an intracellular carrier of bile salts in the epithelial cells of the distal sm ...

    Besides aiding digestion, bile salts are important signal molecules exhibiting a regulatory role in metabolic processes. Human ileal bile acid binding protein (I-BABP) is an intracellular carrier of bile salts in the epithelial cells of the distal small intestine and has a key role in the enterohepatic circulation of bile salts. Positive binding cooperativity combined with site selectivity of glycocholate and glycochenodeoxycholate, the two most abundant bile salts in the human body, make human I-BABP a unique member of the family of intracellular lipid binding proteins. Solution NMR structure of the ternary complex of human I-BABP with glycocholate and glycochenodeoxycholate reveals an extensive network of hydrogen bonds and hydrophobic interactions stabilizing the bound bile salts. Conformational changes accompanying bile salt binding affects four major regions in the protein including the C/D, E/F and G/H loops as well as the helical segment. Most of these protein regions coincide with a previously described network of millisecond time scale fluctuations in the apo protein, a motion absent in the bound state. Comparison of the heterotypic doubly ligated complex with the unligated form provides further evidence of a conformation selection mechanism of ligand entry. Structural and dynamic aspects of human I-BABP-bile salt interaction are discussed and compared with characteristics of ligand binding in other members of the intracellular lipid binding protein family.


    Related Citations: 
    • Internal motions and exchange processes in human ileal bile acid binding protein as studied by backbone (15)N nuclear magnetic resonance spectroscopy
      Horvath, G.,Kiraly, P.,Tarkanyi, G.,Toke, O.
      (2012) Biochemistry 51: 1848
    • A single hydroxyl group governs ligand site selectivity in human ileal bile acid binding protein.
      Tochtrop, G.P.,DeKoster, G.T.,Covey, D.F.,Cistola, D.P.
      (2004) J.Am.Chem.Soc. 126: 11024
    • Internal motions and exchange processes in human ileal bile acid binding protein as studied by backbone (15)N nuclear magnetic resonance spectroscopy.
      Horvath, G.,Kiraly, P.,Tarkanyi, G.,Toke, O.
      (2012) Biochemistry 51: 1848
    • Determinants of cooperativity and site selectivity in human ileal bile acid binding protein.
      Toke, O.,Monsey, J.D.,DeKoster, G.T.,Tochtrop, G.P.,Tang, C.,Cistola, D.P.
      (2006) Biochemistry 45: 727
    • Kinetic mechanism of ligand binding in human ileal bile acid binding protein as determined by stopped-flow fluorescence analysis.
      Toke, O.,Monsey, J.D.,Cistola, D.P.
      (2007) Biochemistry 46: 5427


    Organizational Affiliation

    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO, USA.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.,Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gastrotropin
A
127Homo sapiensMutation(s): 0 
Gene Names: FABP6 (ILBP, ILLBP)
Find proteins for P51161 (Homo sapiens)
Go to Gene View: FABP6
Go to UniProtKB:  P51161
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCH
Query on GCH

Download SDF File 
Download CCD File 
A
GLYCOCHOLIC ACID
N-CHOLYLGLYCINE
C26 H43 N O6
RFDAIACWWDREDC-FRVQLJSFSA-N
 Ligand Interaction
CHO
Query on CHO

Download SDF File 
Download CCD File 
A
GLYCOCHENODEOXYCHOLIC ACID
C26 H43 N O5
GHCZAUBVMUEKKP-GYPHWSFCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2015-12-30
    Type: Database references
  • Version 1.2: 2018-10-17
    Type: Data collection, Database references