3W15

Structure of peroxisomal targeting signal 2 (PTS2) of Saccharomyces cerevisiae 3-ketoacyl-CoA thiolase in complex with Pex7p and Pex21p


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of peroxisomal targeting signal-2 bound to its receptor complex Pex7p-Pex21p

Pan, D.Nakatsu, T.Kato, H.

(2013) Nat.Struct.Mol.Biol. 20: 987-993

  • DOI: 10.1038/nsmb.2618

  • PubMed Abstract: 
  • Appropriate targeting of matrix proteins to peroxisomes is mainly directed by two types of peroxisomal targeting signals, PTS1 and PTS2. Although the basis of PTS1 recognition has been revealed by structural studies, that of PTS2 recognition remains ...

    Appropriate targeting of matrix proteins to peroxisomes is mainly directed by two types of peroxisomal targeting signals, PTS1 and PTS2. Although the basis of PTS1 recognition has been revealed by structural studies, that of PTS2 recognition remains elusive. Here we present the crystal structure of a heterotrimeric PTS2-recognition complex from Saccharomyces cerevisiae, containing Pex7p, the C-terminal region of Pex21p and the PTS2 of the peroxisomal 3-ketoacyl-CoA thiolase. Pex7p forms a β-propeller structure and provides a platform for cooperative interactions with both the amphipathic PTS2 helix and Pex21p. The C-terminal region of Pex21p directly covers the hydrophobic surfaces of both Pex7p and PTS2, and the resulting hydrophobic core is the primary determinant of stable complex formation. Together with in vivo and in vitro functional assays of Pex7p and Pex21p variants, our findings reveal the molecular mechanism of PTS2 recognition.


    Organizational Affiliation

    Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan. pan.dongqing@pharm.kyoto-u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisomal targeting signal 2 receptor
A
368Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PEX7 (PAS7, PEB1)
Find proteins for P39108 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: PEX7
Go to UniProtKB:  P39108
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peroxisomal membrane protein PEX21
B
101Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PEX21
Find proteins for P50091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P50091
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
3-ketoacyl-CoA thiolase, peroxisomal, Maltose-binding periplasmic protein
C
389Escherichia coli (strain K12)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
This entity is chimeric
Mutation(s): 0 
Gene Names: malE, POT1 (FOX3, POX3)
EC: 2.3.1.16
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Find proteins for P27796 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: POT1
Go to UniProtKB:  P27796
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A, B, C
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 78.890α = 90.00
b = 52.750β = 106.59
c = 97.570γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-10-16
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Refinement description, Source and taxonomy