4LMG

Crystal structure of AFT2 in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular mechanism and structure of the Saccharomyces cerevisiae iron regulator Aft2.

Poor, C.B.Wegner, S.V.Li, H.Dlouhy, A.C.Schuermann, J.P.Sanishvili, R.Hinshaw, J.R.Riggs-Gelasco, P.J.Outten, C.E.He, C.

(2014) Proc.Natl.Acad.Sci.USA 111: 4043-4048

  • DOI: 10.1073/pnas.1318869111

  • PubMed Abstract: 
  • The paralogous iron-responsive transcription factors Aft1 and Aft2 (activators of ferrous transport) regulate iron homeostasis in Saccharomyces cerevisiae by activating expression of iron-uptake and -transport genes when intracellular iron is low. We ...

    The paralogous iron-responsive transcription factors Aft1 and Aft2 (activators of ferrous transport) regulate iron homeostasis in Saccharomyces cerevisiae by activating expression of iron-uptake and -transport genes when intracellular iron is low. We present the previously unidentified crystal structure of Aft2 bound to DNA that reveals the mechanism of DNA recognition via specific interactions of the iron-responsive element with a Zn(2+)-containing WRKY-GCM1 domain in Aft2. We also show that two Aft2 monomers bind a [2Fe-2S] cluster (or Fe(2+)) through a Cys-Asp-Cys motif, leading to dimerization of Aft2 and decreased DNA-binding affinity. Furthermore, we demonstrate that the [2Fe-2S]-bridged heterodimer formed between glutaredoxin-3 and the BolA-like protein Fe repressor of activation-2 transfers a [2Fe-2S] cluster to Aft2 that facilitates Aft2 dimerization. Previous in vivo findings strongly support the [2Fe-2S] cluster-induced dimerization model; however, given the available evidence, Fe(2+)-induced Aft2 dimerization cannot be completely ruled out as an alternative Aft2 inhibition mechanism. Taken together, these data provide insight into the molecular mechanism for iron-dependent transcriptional regulation of Aft2 and highlight the key role of Fe-S clusters as cellular iron signals.


    Organizational Affiliation

    Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Iron-regulated transcriptional activator AFT2
A, B, C, D
157Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: AFT2
Find proteins for Q08957 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08957
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*AP*AP*TP*GP*GP*GP*TP*GP*CP*AP*CP*T)-3'E,G13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*AP*AP*GP*TP*GP*CP*AP*CP*CP*CP*AP*TP*T)-3'F,H13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.536α = 90.00
b = 127.453β = 90.04
c = 70.766γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata scaling
PHENIXphasing
PHENIXmodel building
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-04-23
    Type: Database references