Ligand Binding Induces Conformational Changes in Human Cellular Retinol-binding Protein 1 (CRBP1) Revealed by Atomic Resolution Crystal Structures

J Biol Chem. 2016 Apr 15;291(16):8528-40. doi: 10.1074/jbc.M116.714535. Epub 2016 Feb 21.

Abstract

Important in regulating the uptake, storage, and metabolism of retinoids, cellular retinol-binding protein 1 (CRBP1) is essential for trafficking vitamin A through the cytoplasm. However, the molecular details of ligand uptake and targeted release by CRBP1 remain unclear. Here we report the first structure of CRBP1 in a ligand-free form as well as ultra-high resolution structures of this protein bound to either all-trans-retinol or retinylamine, the latter a therapeutic retinoid that prevents light-induced retinal degeneration. Superpositioning of human apo- and holo-CRBP1 revealed major differences within segments surrounding the entrance to the retinoid-binding site. These included α-helix II and hairpin turns between β-strands βC-βD and βE-βF as well as several side chains, such as Phe-57, Tyr-60, and Ile-77, that change their orientations to accommodate the ligand. Additionally, we mapped hydrogen bond networks inside the retinoid-binding cavity and demonstrated their significance for the ligand affinity. Analyses of the crystallographic B-factors indicated several regions with higher backbone mobility in the apoprotein that became more rigid upon retinoid binding. This conformational flexibility of human apo-CRBP1 facilitates interaction with the ligands, whereas the more rigid holoprotein structure protects the labile retinoid moiety during vitamin A transport. These findings suggest a mechanism of induced fit upon ligand binding by mammalian cellular retinol-binding proteins.

Keywords: lipid transport; retinal metabolism; retinoid-binding protein; retinol; vitamin A.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Crystallography, X-Ray
  • Humans
  • Hydrogen Bonding
  • Ligands
  • Protein Structure, Secondary
  • Retinol-Binding Proteins, Cellular / chemistry*
  • Vitamin A / chemistry*

Substances

  • Ligands
  • RBP1 protein, human
  • Retinol-Binding Proteins, Cellular
  • Vitamin A

Associated data

  • PDB/1CRB
  • PDB/4QZT
  • PDB/5H8T
  • PDB/5H9A
  • PDB/5HA1
  • PDB/5HBS