2OE1 | pdb_00002oe1

Crystal Structure of Mitochondrial Thioredoxin 3 from Saccharomyces cerevisiae (reduced form)

• PDB DOI: https://doi.org/10.2210/pdb2OE1/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-12-28 Released: 2008-01-08 
• Deposition Author(s): Bao, R., Zhang, Y.R., Zhou, C.Z., Chen, Y.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.220 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.160 (Depositor) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Structural and mechanistic analyses of yeast mitochondrial thioredoxin Trx3 reveal putative function of its additional cysteine residues

Bao, R., Zhang, Y.R., Zhou, C.-Z., Chen, Y.X.

(2009) Biochim Biophys Acta 1794: 716-721

• PubMed: 19166985 
• DOI: https://doi.org/10.1016/j.bbapap.2008.12.016
• Primary Citation Related Structures: 
  2OE0, 2OE1, 2OE3


• PubMed Abstract: 
  

  The yeast Saccharomyces cerevisiae Trx3 is a key member of the thioredoxin system to control the cellular redox homeostasis in mitochondria. We solved the crystal structures of yeast Trx3 in oxidized and reduced forms at 1.80 and 2.10 A, respectively. Besides the active site, the additional cysteine residue Cys69 also undergoes a significant redox-correlated conformational change. Comparative structural analyses in combination with activity assays revealed that residue Cys69 could be S-nitrosylated in vitro. S-nitrosylation of Cys69 will decrease the activity of Trx3 by 20%, which is comparable to the effect of the Cys69Ser mutation. Taken together, these findings provided us some new insights into the putative function of the additional cysteine residues of Trx3.

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Organizational Affiliation: 
• Institute of Protein Research, Tongji University, Shanghai 200092, PR China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 26.03 kDa 
• Atom Count: 1,851 
• Modeled Residue Count: 212 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin-3	A, B	114	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: TRX3
UniProt
Find proteins for P25372 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25372  Go to UniProtKB:  P25372

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.220 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.160 (Depositor) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.575	α = 90
b = 49.575	β = 90
c = 94.554	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-08 
Deposition Author(s): Bao, R., Zhang, Y.R., Zhou, C.Z., Chen, Y.X.

Revision History  

• Version 1.0: 2008-01-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description