4OO7

THE 1.55A CRYSTAL STRUCTURE of NAF1 (MINER1): THE REDOX-ACTIVE 2FE-2S PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A point mutation in the [2Fe-2S] cluster binding region of the NAF-1 protein (H114C) dramatically hinders the cluster donor properties.

Tamir, S.Eisenberg-Domovich, Y.Conlan, A.R.Stofleth, J.T.Lipper, C.H.Paddock, M.L.Mittler, R.Jennings, P.A.Livnah, O.Nechushtai, R.

(2014) Acta Crystallogr.,Sect.D 70: 1572-1578

  • DOI: 10.1107/S1399004714005458
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NAF-1 is an important [2Fe-2S] NEET protein associated with human health and disease. A mis-splicing mutation in NAF-1 results in Wolfram Syndrome type 2, a lethal childhood disease. Upregulation of NAF-1 is found in epithelial breast cancer cells, a ...

    NAF-1 is an important [2Fe-2S] NEET protein associated with human health and disease. A mis-splicing mutation in NAF-1 results in Wolfram Syndrome type 2, a lethal childhood disease. Upregulation of NAF-1 is found in epithelial breast cancer cells, and suppression of NAF-1 expression by knockdown significantly suppresses tumor growth. Key to NAF-1 function is the NEET fold with its [2Fe-2S] cluster. In this work, the high-resolution structure of native NAF-1 was determined to 1.65 Å resolution (R factor = 13.5%) together with that of a mutant in which the single His ligand of its [2Fe-2S] cluster, His114, was replaced by Cys. The NAF-1 H114C mutant structure was determined to 1.58 Å resolution (R factor = 16.0%). All structural differences were localized to the cluster binding site. Compared with native NAF-1, the [2Fe-2S] clusters of the H114C mutant were found to (i) be 25-fold more stable, (ii) have a redox potential that is 300 mV more negative and (iii) have their cluster donation/transfer function abolished. Because no global structural differences were found between the mutant and the native (wild-type) NAF-1 proteins, yet significant functional differences exist between them, the NAF-1 H114C mutant is an excellent tool to decipher the underlying biological importance of the [2Fe-2S] cluster of NAF-1 in vivo.


    Organizational Affiliation

    The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CDGSH iron-sulfur domain-containing protein 2
A, B
68Homo sapiensMutation(s): 1 
Gene Names: CISD2 (CDGSH2, ERIS, ZCD2)
Find proteins for Q8N5K1 (Homo sapiens)
Go to Gene View: CISD2
Go to UniProtKB:  Q8N5K1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download SDF File 
Download CCD File 
A, B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.135 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.009α = 90.00
b = 48.652β = 90.00
c = 73.730γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data collection
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release