4BWF

Pex4p-Pex22p disulphide bond mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Disulphide Bond in the E2 Enzyme Pex4P Modulates Ubiquitin-Conjugating Activity

Williams, C.van den Berg, M.Stanley, W.A.Wilmanns, M.Distel, B.

(2013) Sci.Rep. 3: 2212

  • DOI: 10.1038/srep02212

  • PubMed Abstract: 
  • The ubiquitin-conjugating enzyme Pex4p together with its binding partner, the peroxisomal membrane protein Pex22p, co-ordinates cysteine-dependent ubiquitination of the cycling receptor protein Pex5p. Unusually for an ubiquitin-conjugating enzyme, Sa ...

    The ubiquitin-conjugating enzyme Pex4p together with its binding partner, the peroxisomal membrane protein Pex22p, co-ordinates cysteine-dependent ubiquitination of the cycling receptor protein Pex5p. Unusually for an ubiquitin-conjugating enzyme, Saccharomyces cerevisiae Pex4p can form a disulphide bond between the cysteine residues at positions 105 and 146. We found that mutating the disulphide forming cysteine residues in Pex4p to serines does not disturb the secondary structure of the protein but does reduce the in vitro activity of Pex4p. From the crystal structure of Pex4p C105S, C146S in complex with the soluble domain of Pex22p, we observe a narrowing of the active site cleft, caused by loss of the disulphide bond. This modification of the active site microenvironment is likely to restrict access of ubiquitin to the active site cysteine, modulating Pex4p activity. Finally, based on sequence and structural alignments, we have identified other ubiquitin-conjugating enzymes that may contain disulphide bonds.


    Organizational Affiliation

    European Molecular Biology Laboratory, Structural Biology Unit, Notkestrasse 85, 22603, Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN-CONJUGATING ENZYME E2-21 KDA
A
172Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 3 
Gene Names: PEX4 (PAS2, UBC10)
EC: 2.3.2.23
Find proteins for P29340 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P29340
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PEROXISOME ASSEMBLY PROTEIN 22
B
130Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PEX22
Find proteins for P39718 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39718
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 138.858α = 90.00
b = 42.802β = 100.14
c = 60.540γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-08-07
    Type: Database references
  • Version 1.2: 2017-12-13
    Type: Database references