5BVS

Linoleate-bound pFABP4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the ligand-binding specificity of fatty acid-binding proteins (pFABP4 and pFABP5) in gentoo penguin

Lee, C.W.Kim, J.E.Do, H.Kim, R.O.Lee, S.G.Park, H.H.Chang, J.H.Yim, J.H.Park, H.Kim, I.C.Lee, J.H.

(2015) Biochem Biophys Res Commun 465: 12-18

  • DOI: 10.1016/j.bbrc.2015.07.087
  • Primary Citation of Related Structures:  
    5BVQ, 5BVT, 5BVS

  • PubMed Abstract: 
  • Fatty acid-binding proteins (FABPs) are involved in transporting hydrophobic fatty acids between various aqueous compartments of the cell by directly binding ligands inside their β-barrel cavities. Here, we report the crystal structures of ligand-unbound pFABP4, linoleate-bound pFABP4, and palmitate-bound pFABP5, obtained from gentoo penguin (Pygoscelis papua), at a resolution of 2 ...

    Fatty acid-binding proteins (FABPs) are involved in transporting hydrophobic fatty acids between various aqueous compartments of the cell by directly binding ligands inside their β-barrel cavities. Here, we report the crystal structures of ligand-unbound pFABP4, linoleate-bound pFABP4, and palmitate-bound pFABP5, obtained from gentoo penguin (Pygoscelis papua), at a resolution of 2.1 Å, 2.2 Å, and 2.3 Å, respectively. The pFABP4 and pFABP5 proteins have a canonical β-barrel structure with two short α-helices that form a cap region and fatty acid ligand binding sites in the hydrophobic cavity within the β-barrel structure. Linoleate-bound pFABP4 and palmitate-bound pFABP5 possess different ligand-binding modes and a unique ligand-binding pocket due to several sequence dissimilarities (A76/L78, T30/M32, underlining indicates pFABP4 residues) between the two proteins. Structural comparison revealed significantly different conformational changes in the β3-β4 loop region (residues 57-62) as well as the flipped Phe60 residue of pFABP5 than that in pFABP4 (the corresponding residue is Phe58). A ligand-binding study using fluorophore displacement assays shows that pFABP4 has a relatively strong affinity for linoleate as compared to pFABP5. In contrast, pFABP5 exhibits higher affinity for palmitate than that for pFABP4. In conclusion, our high-resolution structures and ligand-binding studies provide useful insights into the ligand-binding preferences of pFABPs based on key protein-ligand interactions.


    Organizational Affiliation

    Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Republic of Korea. Electronic address: junhyucklee@kopri.re.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fatty acid-binding proteinA, B132Pygoscelis papuaMutation(s): 0 
Gene Names: FABP4
UniProt
Find proteins for A0A0K0MJN3 (Pygoscelis papua)
Explore A0A0K0MJN3 
Go to UniProtKB:  A0A0K0MJN3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EIC
Query on EIC

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]LINOLEIC ACID
C18 H32 O2
OYHQOLUKZRVURQ-HZJYTTRNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.487α = 90
b = 60.487β = 90
c = 139.569γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
HKL-2000data processing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Database references