2B5E

Crystal Structure of Yeast Protein Disulfide Isomerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 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
  • Primary Citation of Related Structures:  
    2B5E

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein disulfide-isomeraseA504Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PDI1MFP1TRG1
EC: 5.3.4.1
Find proteins for P17967 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17967 
Go to UniProtKB:  P17967
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BA
Query on BA

Download CCD File 
A
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.191 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.56α = 90
b = 136.56β = 90
c = 69.524γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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