2B5E

Crystal Structure of Yeast Protein Disulfide Isomerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of yeast protein disulfide isomerase suggests cooperativity between its active sites.

Tian, G.Xiang, S.Noiva, R.Lennarz, W.J.Schindelin, H.

(2006) Cell 124: 61-73

  • DOI: 10.1016/j.cell.2005.10.044

  • PubMed Abstract: 
  • Protein disulfide isomerase plays a key role in catalyzing the folding of secretory proteins. It features two catalytically inactive thioredoxin domains inserted between two catalytically active thioredoxin domains and an acidic C-terminal tail. The ...

    Protein disulfide isomerase plays a key role in catalyzing the folding of secretory proteins. It features two catalytically inactive thioredoxin domains inserted between two catalytically active thioredoxin domains and an acidic C-terminal tail. The crystal structure of yeast PDI reveals that the four thioredoxin domains are arranged in the shape of a twisted "U" with the active sites facing each other across the long sides of the "U." The inside surface of the "U" is enriched in hydrophobic residues, thereby facilitating interactions with misfolded proteins. The domain arrangement, active site location, and surface features strikingly resemble the Escherichia coli DsbC and DsbG protein disulfide isomerases. Biochemical studies demonstrate that all domains of PDI, including the C-terminal tail, are required for full catalytic activity. The structure defines a framework for rationalizing the differences between the two active sites and their respective roles in catalyzing the formation and rearrangement of disulfide bonds.


    Organizational Affiliation

    Department of Biochemistry and Cell Biology, State University of New York at Stony Brook, NY 11794, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein disulfide-isomerase
A
504Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PDI1 (MFP1, TRG1)
EC: 5.3.4.1
Find proteins for P17967 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17967
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BA
Query on BA

Download SDF File 
Download CCD File 
A
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.191 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 136.560α = 90.00
b = 136.560β = 90.00
c = 69.524γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance