Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 94.42 kDa 
• Atom Count: 7348 
• Modelled Residue Count: 826 
• Deposited Residue Count: 858 
• Unique protein chains: 1

4Q75

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

• PDB DOI: 10.2210/pdb4Q75/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-24 Released: 2014-09-10 
• Deposition Author(s): Roret, T., Didierjean, C.

---

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 

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

• PubMed: 25195888 
• DOI: 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase 2, chloroplastic	A, B	429	Arabidopsis thaliana	Mutation(s): 0  Gene Names: NFS2, NIFS, At1g08490, T27G7.17, CpNIFS, CpNIFS1 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

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A, B	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

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 = 81.567	α = 90
b = 68.205	β = 94.76
c = 87.066	γ = 90

Software Package:

Software Name	Purpose
Xnemo	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-04-24 
• Released Date: 2014-09-10 
Deposition Author(s): Roret, T., Didierjean, C.

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references