5CRW

Crystal structure of the b'-a' domain of oxidized protein disulfide isomerase complexed with alpha-synuclein peptide (31-41)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of redox-dependent substrate binding of protein disulfide isomerase.

Yagi-Utsumi, M.Satoh, T.Kato, K.

(2015) Sci Rep 5: 13909-13909

  • DOI: 10.1038/srep13909

  • PubMed Abstract: 
  • Protein disulfide isomerase (PDI) is a multidomain enzyme, operating as an essential folding catalyst, in which the b' and a' domains provide substrate binding sites and undergo an open-closed domain rearrangement depending on the redox states of the ...

    Protein disulfide isomerase (PDI) is a multidomain enzyme, operating as an essential folding catalyst, in which the b' and a' domains provide substrate binding sites and undergo an open-closed domain rearrangement depending on the redox states of the a' domain. Despite the long research history of this enzyme, three-dimensional structural data remain unavailable for its ligand-binding mode. Here we characterize PDI substrate recognition using α-synuclein (αSN) as the model ligand. Our nuclear magnetic resonance (NMR) data revealed that the substrate-binding domains of PDI captured the αSN segment Val37-Val40 only in the oxidized form. Furthermore, we determined the crystal structure of an oxidized form of the b'-a' domains in complex with an undecapeptide corresponding to this segment. The peptide-binding mode observed in the crystal structure with NMR validation, was characterized by hydrophobic interactions on the b' domain in an open conformation. Comparison with the previously reported crystal structure indicates that the a' domain partially masks the binding surface of the b' domain, causing steric hindrance against the peptide in the reduced form of the b'-a' domains that exhibits a closed conformation. These findings provide a structural basis for the mechanism underlying the redox-dependent substrate binding of PDI.


    Organizational Affiliation

    Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein disulfide-isomerase
A
247Humicola insolensMutation(s): 0 
EC: 5.3.4.1
Find proteins for P55059 (Humicola insolens)
Go to UniProtKB:  P55059
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide from Alpha-synuclein
B
11Homo sapiensMutation(s): 0 
Gene Names: SNCA (NACP, PARK1)
Find proteins for P37840 (Homo sapiens)
Go to Gene View: SNCA
Go to UniProtKB:  P37840
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.753α = 90.00
b = 62.510β = 90.00
c = 68.156γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPS/MEXTJapan15K21680, 24770102, 25102001, 25102008, 25121730

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Database references
  • Version 1.2: 2018-02-07
    Type: Data collection, Database references, Derived calculations