3CV0

Structure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei Peroxin 5 (TbPEX5)complexed to T. brucei Phosphoglucoisomerase (PGI) PTS1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Insights into the recognition of peroxisomal targeting signal 1 by Trypanosoma brucei peroxin 5.

Sampathkumar, P.Roach, C.Michels, P.A.Hol, W.G.

(2008) J.Mol.Biol. 381: 867-880

  • DOI: 10.1016/j.jmb.2008.05.089
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycosomes are peroxisome-like organelles essential for trypanosomatid parasites. Glycosome biogenesis is mediated by proteins called "peroxins," which are considered to be promising drug targets in pathogenic Trypanosomatidae. The first step during ...

    Glycosomes are peroxisome-like organelles essential for trypanosomatid parasites. Glycosome biogenesis is mediated by proteins called "peroxins," which are considered to be promising drug targets in pathogenic Trypanosomatidae. The first step during protein translocation across the glycosomal membrane of peroxisomal targeting signal 1 (PTS1)-harboring proteins is signal recognition by the cytosolic receptor peroxin 5 (PEX5). The C-terminal PTS1 motifs interact with the PTS1 binding domain (P1BD) of PEX5, which is made up of seven tetratricopeptide repeats. Obtaining diffraction-quality crystals of the P1BD of Trypanosoma brucei PEX5 (TbPEX5) required surface entropy reduction mutagenesis. Each of the seven tetratricopeptide repeats appears to have a residue in the alpha(L) conformation in the loop connecting helices A and B. Five crystal structures of the P1BD of TbPEX5 were determined, each in complex with a hepta- or decapeptide corresponding to a natural or nonnatural PTS1 sequence. The PTS1 peptides are bound between the two subdomains of the P1BD. These structures indicate precise recognition of the C-terminal Leu of the PTS1 motif and important interactions between the PTS1 peptide main chain and up to five invariant Asn side chains of PEX5. The TbPEX5 structures reported here reveal a unique hydrophobic pocket in the subdomain interface that might be explored to obtain compounds that prevent relative motions of the subdomains and interfere selectively with PTS1 motif binding or release in trypanosomatids, and would therefore disrupt glycosome biogenesis and prevent parasite growth.


    Organizational Affiliation

    Department of Biochemistry, Biomolecular Structure Center, University of Washington, Box 357742, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome targeting signal 1 receptor PEX5
A
327Trypanosoma brucei brucei (strain 927/4 GUTat10.1)Mutation(s): 2 
Find proteins for Q57W55 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Go to UniProtKB:  Q57W55
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
T. brucei PGI PTS1 peptide Ac-FNELSHL
B
7Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: PGI
EC: 5.3.1.9
Find proteins for P13377 (Trypanosoma brucei brucei)
Go to UniProtKB:  P13377
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.405α = 90.00
b = 66.404β = 104.47
c = 52.117γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
d*TREKdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-01-24
    Type: Structure summary