Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.17 kDa 
• Atom Count: 1066 
• Residue Count: 127 
• Unique protein chains: 1

2MM3

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

• DOI: 10.2210/pdb2MM3/pdb
• BMRB: 19843

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-07 Released: 2014-05-07 
• Deposition Author(s): Horvath, G., Egyed, O., Bencsura, A., Simon, A., Tochtrop, G.P., DeKoster, G.T., Covey, D.F., Cistola, D.P., Toke, O.

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Experimental Data Snapshot

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

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

• PubMed: 26613247 
• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gastrotropin	A	127	Homo sapiens	Mutation(s): 0  Gene Names: FABP6, ILBP, ILLBP
Find proteins for P51161 (Homo sapiens) Explore P51161  Go to UniProtKB:  P51161
NIH Common Fund Data Resources
PHAROS:  P51161 GTEx:  ENSG00000170231

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GCH	A	GLYCOCHOLIC ACID C26 H43 N O6 RFDAIACWWDREDC-FRVQLJSFSA-N
CHO	A	GLYCOCHENODEOXYCHOLIC ACID C26 H43 N O5 GHCZAUBVMUEKKP-GYPHWSFCSA-N

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

Entry History 

Deposition Data

• Deposited Date: 2014-03-07 
• Released Date: 2014-05-07 
Deposition Author(s): Horvath, G., Egyed, O., Bencsura, A., Simon, A., Tochtrop, G.P., DeKoster, G.T., Covey, D.F., Cistola, D.P., Toke, O.

Revision History 

• 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