7NCV | pdb_00007ncv

Crystal structure of reduced glutaredoxin 2 from Chlamydomonas reinhardtii

• PDB DOI: https://doi.org/10.2210/pdb7NCV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Chlamydomonas reinhardtii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-01-29 Released: 2021-05-26 
• Deposition Author(s): Roret, T., Didierjean, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.180 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Atypical Iron-Sulfur Cluster Binding, Redox Activity and Structural Properties of Chlamydomonas reinhardtii Glutaredoxin 2.

Roret, T., Zhang, B., Moseler, A., Dhalleine, T., Gao, X.H., Couturier, J., Lemaire, S.D., Didierjean, C., Johnson, M.K., Rouhier, N.

(2021) Antioxidants (Basel) 10

• PubMed: 34069657 
• DOI: https://doi.org/10.3390/antiox10050803
• Primary Citation Related Structures: 
  7NCV, 7NCW


• PubMed Abstract: 
  

  Glutaredoxins (GRXs) are thioredoxin superfamily members exhibiting thiol-disulfide oxidoreductase activity and/or iron-sulfur (Fe-S) cluster binding capacities. These properties are determined by specific structural factors. In this study, we examined the capacity of the class I Chlamydomonas reinhardtii GRX2 recombinant protein to catalyze both protein glutathionylation and deglutathionylation reactions using a redox sensitive fluorescent protein as a model protein substrate. We observed that the catalytic cysteine of the CPYC active site motif of GRX2 was sufficient for catalyzing both reactions in the presence of glutathione. Unexpectedly, spectroscopic characterization of the protein purified under anaerobiosis showed the presence of a [2Fe-2S] cluster despite having a presumably inadequate active site signature, based on past mutational analyses. The spectroscopic characterization of cysteine mutated variants together with modeling of the Fe-S cluster-bound GRX homodimer from the structure of an apo-GRX2 indicate the existence of an atypical Fe-S cluster environment and ligation mode. Overall, the results further delineate the biochemical and structural properties of conventional GRXs, pointing to the existence of multiple factors more complex than anticipated, sustaining the capacity of these proteins to bind Fe-S clusters.

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Organizational Affiliation: 
• Université de Lorraine, INRAE, IAM, F-54000 Nancy, France.
Department of Chemistry and Centre for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA.
Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, USA.
Institut de Biologie Paris-Seine, Laboratoire de Biologie Computationnelle et Quantitative, Sorbonne Université, CNRS, UMR7238, 75006 Paris, France.
Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Sorbonne Université, CNRS, UMR8226, 75006 Paris, France.
Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 11.46 kDa 
• Atom Count: 973 
• Modeled Residue Count: 107 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaredoxin, CPYC type	A	107	Chlamydomonas reinhardtii	Mutation(s): 0  Gene Names: GRX2, CHLRE_12g550400v5, CHLREDRAFT_195611
UniProt
Find proteins for A8IYH1 (Chlamydomonas reinhardtii) Explore A8IYH1  Go to UniProtKB:  A8IYH1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.180 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.648	α = 90
b = 45.648	β = 90
c = 104.667	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
Coot	model building
MOLREP	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-26 
Deposition Author(s): Roret, T., Didierjean, C.

Revision History  

• Version 1.0: 2021-05-26
  Type: Initial release
  
• Version 1.1: 2021-06-16
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary