5VHG

Crystal structure of pentad mutant GAPR-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural insights into the interaction of the conserved mammalian proteins GAPR-1 and Beclin 1, a key autophagy protein.

Li, Y.Zhao, Y.Su, M.Glover, K.Chakravarthy, S.Colbert, C.L.Levine, B.Sinha, S.C.

(2017) Acta Crystallogr D Struct Biol 73: 775-792

  • DOI: 10.1107/S2059798317011822

  • PubMed Abstract: 
  • Mammalian Golgi-associated plant pathogenesis-related protein 1 (GAPR-1) is a negative autophagy regulator that binds Beclin 1, a key component of the autophagosome nucleation complex. Beclin 1 residues 267-284 are required for binding GAPR-1. Here, ...

    Mammalian Golgi-associated plant pathogenesis-related protein 1 (GAPR-1) is a negative autophagy regulator that binds Beclin 1, a key component of the autophagosome nucleation complex. Beclin 1 residues 267-284 are required for binding GAPR-1. Here, sequence analyses, structural modeling, mutagenesis combined with pull-down assays, X-ray crystal structure determination and small-angle X-ray scattering were used to investigate the Beclin 1-GAPR-1 interaction. Five conserved residues line an equatorial GAPR-1 surface groove that is large enough to bind a peptide. A model of a peptide comprising Beclin 1 residues 267-284 docked onto GAPR-1, built using the CABS-dock server, indicates that this peptide binds to this GAPR-1 groove. Mutation of the five conserved residues lining this groove, H54A/E86A/G102K/H103A/N138G, abrogates Beclin 1 binding. The 1.27 Å resolution X-ray crystal structure of this pentad mutant GAPR-1 was determined. Comparison with the wild-type (WT) GAPR-1 structure shows that the equatorial groove of the pentad mutant is shallower and more positively charged, and therefore may not efficiently bind Beclin 1 residues 267-284, which include many hydrophobic residues. Both WT and pentad mutant GAPR-1 crystallize as dimers, and in each case the equatorial groove of one subunit is partially occluded by the other subunit, indicating that dimeric GAPR-1 is unlikely to bind Beclin 1. SAXS analysis of WT and pentad mutant GAPR-1 indicates that in solution the WT forms monomers, while the pentad mutant is primarily dimeric. Thus, changes in the structure of the equatorial groove combined with the improved dimerization of pentad mutant GAPR-1 are likely to abrogate binding to Beclin 1.


    Organizational Affiliation

    Bio-CAT, Advanced Photon Source, 9700 South Cass Avenue, LSEP Building 435B, Argonne, IL 60439, USA.,Center for Autophagy Research, Department of Internal Medicine and Microbiology, UT Southwestern Medical Center and Howard Hughes Medical Institute, Dallas, TX 75390, USA.,Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Golgi-associated plant pathogenesis-related protein 1
A
150Homo sapiensMutation(s): 5 
Gene Names: GLIPR2 (C9orf19, GAPR1)
Find proteins for Q9H4G4 (Homo sapiens)
Go to Gene View: GLIPR2
Go to UniProtKB:  Q9H4G4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.150 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 62.307α = 90.00
b = 84.665β = 90.00
c = 51.426γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
AUTOMARdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release