4Q75

Crystal structure of Nfs2, the plastidial cysteine desulfurase from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

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This is version 1.3 of the entry. See complete history


Literature

X-ray structures of Nfs2, the plastidial cysteine desulfurase from Arabidopsis thaliana.

Roret, T.Pegeot, H.Couturier, J.Mulliert, G.Rouhier, N.Didierjean, C.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 1180-1185

  • DOI: https://doi.org/10.1107/S2053230X14017026
  • Primary Citation of Related Structures:  
    4Q75, 4Q76

  • PubMed Abstract: 

    The chloroplastic Arabidopsis thaliana Nfs2 (AtNfs2) is a group II pyridoxal 5'-phosphate-dependent cysteine desulfurase that is involved in the initial steps of iron-sulfur cluster biogenesis. The group II cysteine desulfurases require the presence of sulfurtransferases such as SufE proteins for optimal activity. Compared with group I cysteine desulfurases, proteins of this group contains a smaller extended lobe harbouring the catalytic cysteine and have a β-hairpin constraining the active site. Here, two crystal structures of AtNfs2 are reported: a wild-type form with the catalytic cysteine in a persulfide-intermediate state and a C384S variant mimicking the resting state of the enzyme. In both structures the well conserved Lys241 covalently binds pyridoxal 5'-phosphate, forming an internal aldimine. Based on available homologous bacterial complexes, a model of a complex between AtNfs2 and the SufE domain of its biological partner AtSufE1 is proposed, revealing the nature of the binding sites.


  • Organizational Affiliation

    Université de Lorraine, UMR 7036 CRM2, BioMod Group, BP 70239, 54506 Vandoeuvre-lès-Nancy, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine desulfurase 2, chloroplastic
A, B
429Arabidopsis thalianaMutation(s): 0 
Gene Names: NFS2NIFSAt1g08490T27G7.17
EC: 2.8.1.7 (PDB Primary Data), 4.4.1.16 (PDB Primary Data)
UniProt
Find proteins for Q93WX6 (Arabidopsis thaliana)
Explore Q93WX6 
Go to UniProtKB:  Q93WX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93WX6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSS
Query on CSS
A, B
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
LLP
Query on LLP
A, B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.567α = 90
b = 68.205β = 94.76
c = 87.066γ = 90
Software Package:
Software NamePurpose
Xnemodata collection
MOLREPphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection