3ED3 | pdb_00003ed3

Crystal Structure of the Yeast Dithiol/Disulfide Oxidoreductase Mpd1p

• PDB DOI: https://doi.org/10.2210/pdb3ED3/pdb

• Classification: ISOMERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-02 Released: 2008-11-04 
• Deposition Author(s): Vitu, E., Greenblatt, H.M., Fass, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.255 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.219 (DCC) 

Literature

Yeast Mpd1p reveals the structural diversity of the protein disulfide isomerase family

Vitu, E., Gross, E., Greenblatt, H.M., Sevier, C.S., Kaiser, C.A., Fass, D.

(2008) J Mol Biology 384: 631-640

• PubMed: 18845159 
• DOI: https://doi.org/10.1016/j.jmb.2008.09.052
• Primary Citation Related Structures: 
  3ED3


• PubMed Abstract: 
  

  Oxidoreductases belonging to the protein disulfide isomerase (PDI) family promote proper disulfide bond formation in substrate proteins in the endoplasmic reticulum. In plants and metazoans, new family members continue to be identified and assigned to various functional niches. PDI-like proteins typically contain tandem thioredoxin-fold domains. The limited information available suggested that the relative orientations of these domains may be quite uniform across the family, and structural models based on this assumption are appearing. However, the X-ray crystal structure of the yeast PDI family protein Mpd1p, described here, demonstrates the radically different domain orientations and surface properties achievable with multiple copies of the thioredoxin fold. A comparison of Mpd1p with yeast Pdi1p expands our perspective on the contexts in which redox-active motifs are presented in the PDI family.

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Organizational Affiliation: 
• Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.24 kDa 
• Atom Count: 4,656 
• Modeled Residue Count: 533 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein disulfide-isomerase MPD1	A, B	298	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: MPD1 EC: 5.3.4.1
UniProt
Find proteins for Q12404 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12404  Go to UniProtKB:  Q12404

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	I [auth A], J [auth A], N [auth B], O [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.255 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.219 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.157	α = 90
b = 92.268	β = 92.23
c = 79.337	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-04 
Deposition Author(s): Vitu, E., Greenblatt, H.M., Fass, D.

Revision History  

• Version 1.0: 2008-11-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary