1RP4

Structure of Ero1p, Source of Disulfide Bonds for Oxidative Protein Folding in the Cell

• PDB DOI: https://doi.org/10.2210/pdb1RP4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2003-12-03 Released: 2004-06-08 
• Deposition Author(s): Gross, E., Kastner, D.B., Kaiser, C.A., Fass, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.244 
• R-Value Work: 0.217 

Literature

Structure of ero1p, source of disulfide bonds for oxidative protein folding in the cell.

Gross, E., Kastner, D.B., Kaiser, C.A., Fass, D.

(2004) Cell 117: 601-610

• PubMed: 15163408 
• DOI: https://doi.org/10.1016/s0092-8674(04)00418-0
• Primary Citation of Related Structures:  
  1RP4, 1RQ1


• PubMed Abstract: 
  

  The flavoenzyme Ero1p produces disulfide bonds for oxidative protein folding in the endoplasmic reticulum. Disulfides generated de novo within Ero1p are transferred to protein disulfide isomerase and then to substrate proteins by dithiol-disulfide exchange reactions. Despite this key role of Ero1p, little is known about the mechanism by which this enzyme catalyzes thiol oxidation. Here, we present the X-ray crystallographic structure of Ero1p, which reveals the molecular details of the catalytic center, the role of a CXXCXXC motif, and the spatial relationship between functionally significant cysteines and the bound cofactor. Remarkably, the Ero1p active site closely resembles that of the versatile thiol oxidase module of Erv2p, a protein with no sequence homology to Ero1p. Furthermore, both Ero1p and Erv2p display essential dicysteine motifs on mobile polypeptide segments, suggesting that shuttling electrons to a rigid active site using a flexible strand is a fundamental feature of disulfide-generating flavoenzymes.

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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.

Macromolecule Content

• Total Structure Weight: 46.32 kDa 
• Atom Count: 3,169 
• Modelled Residue Count: 374 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical 65.0 kDa protein in COX14-COS3 intergenic region precursor	A	389	Saccharomyces cerevisiae	Mutation(s): 7  Gene Names: YML130C, YM4987.05C EC: 1.8.4 Membrane Entity: Yes
UniProt
Find proteins for Q03103 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03103  Go to UniProtKB:  Q03103

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NEN	D [auth A]	1-ETHYL-PYRROLIDINE-2,5-DIONE C6 H9 N O2 GHAZCVNUKKZTLG-UHFFFAOYSA-N
CD	B [auth A], C [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.244 
• R-Value Work: 0.217 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.47	α = 90
b = 134.33	β = 90
c = 102.68	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-08 
Deposition Author(s): Gross, E., Kastner, D.B., Kaiser, C.A., Fass, D.

Revision History  

• Version 1.0: 2004-06-08
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation