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
  • Primary Citation of Related Structures:  
    2MM3

  • 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 small intestine and has a key role in the enterohepatic circulation of bile salts ...

    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: 
    • 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
    • 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
    • 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
    • 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
    • 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

    Organizational Affiliation

    Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GastrotropinA127Homo sapiensMutation(s): 0 
Gene Names: FABP6ILBPILLBP
UniProt & NIH Common Fund Data Resources
Find proteins for P51161 (Homo sapiens)
Explore P51161 
Go to UniProtKB:  P51161
PHAROS:  P51161
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCH (Subject of Investigation/LOI)
Query on GCH

Download Ideal Coordinates CCD File 
B [auth A]GLYCOCHOLIC ACID
C26 H43 N O6
RFDAIACWWDREDC-FRVQLJSFSA-N
 Ligand Interaction
CHO (Subject of Investigation/LOI)
Query on CHO

Download Ideal Coordinates CCD File 
C [auth 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 
  • OLDERADO: 2MM3 Olderado

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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