3EBB

PLAP/P97 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and function of the PLAA/Ufd3-p97/Cdc48 complex.

Qiu, L.Pashkova, N.Walker, J.R.Winistorfer, S.Allali-Hassani, A.Akutsu, M.Piper, R.Dhe-Paganon, S.

(2010) J.Biol.Chem. 285: 365-372

  • DOI: 10.1074/jbc.M109.044685

  • PubMed Abstract: 
  • PLAA (ortholog of yeast Doa1/Ufd3, also know as human PLAP or phospholipase A2-activating protein) has been implicated in a variety of disparate biological processes that involve the ubiquitin system. It is linked to the maintenance of ubiquitin leve ...

    PLAA (ortholog of yeast Doa1/Ufd3, also know as human PLAP or phospholipase A2-activating protein) has been implicated in a variety of disparate biological processes that involve the ubiquitin system. It is linked to the maintenance of ubiquitin levels, but the mechanism by which it accomplishes this is unclear. The C-terminal PUL (PLAP, Ufd3p, and Lub1p) domain of PLAA binds p97, an AAA ATPase, which among other functions helps transfer ubiquitinated proteins to the proteasome for degradation. In yeast, loss of Doa1 is suppressed by altering p97/Cdc48 function indicating that physical interaction between PLAA and p97 is functionally important. Although the overall regions of interaction between these proteins are known, the structural basis has been unavailable. We solved the high resolution crystal structure of the p97-PLAA complex showing that the PUL domain forms a 6-mer Armadillo-containing domain. Its N-terminal extension folds back onto the inner curvature forming a deep ridge that is positively charged with residues that are phylogenetically conserved. The C terminus of p97 binds in this ridge, where the side chain of p97-Tyr(805), implicated in phosphorylation-dependent regulation, is buried. Expressed in doa1Delta null cells, point mutants of the yeast ortholog Doa1 that disrupt this interaction display slightly reduced ubiquitin levels, but unlike doa1Delta null cells, showed only some of the growth phenotypes. These data suggest that the p97-PLAA interaction is important for a subset of PLAA-dependent biological processes and provides a framework to better understand the role of these complex molecules in the ubiquitin system.


    Organizational Affiliation

    Structural Genomics Consortium, Department of Physiology, University of Toronto, Toronto, Ontario M5G 1L7,Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2-ACTIVATING PROTEIN
A, B, C, D
304Homo sapiensMutation(s): 0 
Gene Names: PLAA (PLAP)
Find proteins for Q9Y263 (Homo sapiens)
Go to Gene View: PLAA
Go to UniProtKB:  Q9Y263
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE (TER ATP
E, F, G, H
10Homo sapiensMutation(s): 0 
Gene Names: VCP
EC: 3.6.4.6
Find proteins for P55072 (Homo sapiens)
Go to Gene View: VCP
Go to UniProtKB:  P55072
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.384α = 90.00
b = 68.651β = 103.45
c = 143.975γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
REFMACrefinement
RESOLVEphasing
RESOLVEmodel building
SOLVEphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-04-02
    Type: Source and taxonomy