5HZQ

Crystal structure of cellular retinoic acid binding protein 2 (CRABP2)-aryl fluorosulfate covalent conjugate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Arylfluorosulfates Inactivate Intracellular Lipid Binding Protein(s) through Chemoselective SuFEx Reaction with a Binding Site Tyr Residue.

Chen, W.Dong, J.Plate, L.Mortenson, D.E.Brighty, G.J.Li, S.Liu, Y.Galmozzi, A.Lee, P.S.Hulce, J.J.Cravatt, B.F.Saez, E.Powers, E.T.Wilson, I.A.Sharpless, K.B.Kelly, J.W.

(2016) J.Am.Chem.Soc. 138: 7353-7364

  • DOI: 10.1021/jacs.6b02960

  • PubMed Abstract: 
  • Arylfluorosulfates have appeared only rarely in the literature and have not been explored as probes for covalent conjugation to proteins, possibly because they were assumed to possess high reactivity, as with other sulfur(VI) halides. However, we fin ...

    Arylfluorosulfates have appeared only rarely in the literature and have not been explored as probes for covalent conjugation to proteins, possibly because they were assumed to possess high reactivity, as with other sulfur(VI) halides. However, we find that arylfluorosulfates become reactive only under certain circumstances, e.g., when fluoride displacement by a nucleophile is facilitated. Herein, we explore the reactivity of structurally simple arylfluorosulfates toward the proteome of human cells. We demonstrate that the protein reactivity of arylfluorosulfates is lower than that of the corresponding aryl sulfonyl fluorides, which are better characterized with regard to proteome reactivity. We discovered that simple hydrophobic arylfluorosulfates selectively react with a few members of the intracellular lipid binding protein (iLBP) family. A central function of iLBPs is to deliver small-molecule ligands to nuclear hormone receptors. Arylfluorosulfate probe 1 reacts with a conserved tyrosine residue in the ligand-binding site of a subset of iLBPs. Arylfluorosulfate probes 3 and 4, featuring a biphenyl core, very selectively and efficiently modify cellular retinoic acid binding protein 2 (CRABP2), both in vitro and in living cells. The X-ray crystal structure of the CRABP2-4 conjugate, when considered together with binding site mutagenesis experiments, provides insight into how CRABP2 might activate arylfluorosulfates toward site-specific reaction. Treatment of breast cancer cells with probe 4 attenuates nuclear hormone receptor activity mediated by retinoic acid, an endogenous client lipid of CRABP2. Our findings demonstrate that arylfluorosulfates can selectively target single iLBPs, making them useful for understanding iLBP function.


    Organizational Affiliation

    Department of Chemistry and §Department of Molecular and Experimental Medicine, ∥Department of Chemical Physiology, ⊥Department of Integrative Structural and Computational Biology, #The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cellular retinoic acid-binding protein 2
A, B
140Homo sapiensMutation(s): 0 
Gene Names: CRABP2
Find proteins for P29373 (Homo sapiens)
Go to Gene View: CRABP2
Go to UniProtKB:  P29373
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
YWZ
Query on YWZ

Download SDF File 
Download CCD File 
A, B
4'-[(3,6,9,12-tetraoxapentadec-14-yn-1-yl)oxy][1,1'-biphenyl]-4-yl sulfurofluoridate
C23 H27 F O8 S
LGGNGJGQVBUVOE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.029α = 90.00
b = 89.732β = 90.00
c = 92.463γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK106582

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-29
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Derived calculations