1JRA

Crystal Structure of Erv2p

• PDB DOI: https://doi.org/10.2210/pdb1JRA/pdb

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


• Deposited: 2001-08-13 Released: 2001-12-28 
• Deposition Author(s): Gross, E., Sevier, C.S., Vala, A., Kaiser, C.A., Fass, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.196 

Starting Model: experimental

Literature

A new FAD-binding fold and intersubunit disulfide shuttle in the thiol oxidase Erv2p.

Gross, E., Sevier, C.S., Vala, A., Kaiser, C.A., Fass, D.

(2002) Nat Struct Biol 9: 61-67

• PubMed: 11740506 
• DOI: https://doi.org/10.1038/nsb740
• Primary Citation of Related Structures:  
  1JR8, 1JRA


• PubMed Abstract: 
  

  Erv2p is an FAD-dependent sulfhydryl oxidase that can promote disulfide bond formation during protein biosynthesis in the yeast endoplasmic reticulum. The structure of Erv2p, determined by X-ray crystallography to 1.5 A resolution, reveals a helix-rich dimer with no global resemblance to other known FAD-binding proteins or thiol oxidoreductases. Two pairs of cysteine residues are required for Erv2p activity. The first (Cys-Gly-Glu-Cys) is adjacent to the isoalloxazine ring of the FAD. The second (Cys-Gly-Cys) is part of a flexible C-terminal segment that can swing into the vicinity of the first cysteine pair in the opposite subunit of the dimer and may shuttle electrons between substrate protein dithiols and the FAD-proximal disulfide.

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Organizational Affiliation: 

Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 57.24 kDa 
• Atom Count: 3,944 
• Modelled Residue Count: 420 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ERV2 PROTEIN, MITOCHONDRIAL	A, B, C, D	117	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: ERV2 EC: 1.8.3.2
UniProt
Find proteins for Q12284 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12284  Go to UniProtKB:  Q12284

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], F [auth B], G [auth C], H [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.63	α = 90
b = 66.81	β = 91.44
c = 60.38	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-12-28 
Deposition Author(s): Gross, E., Sevier, C.S., Vala, A., Kaiser, C.A., Fass, D.

Revision History  

• Version 1.0: 2001-12-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary