4JY8

X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.901 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters.

Nicolet, Y.Rohac, R.Martin, L.Fontecilla-Camps, J.C.

(2013) Proc.Natl.Acad.Sci.USA 110: 7188-7192

  • DOI: 10.1073/pnas.1302388110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fe4S4 clusters are very common versatile prosthetic groups in proteins. Their redox property of being sensitive to O2-induced oxidative damage is, for instance, used by the cell to sense oxygen levels and switch between aerobic and anaerobic metaboli ...

    Fe4S4 clusters are very common versatile prosthetic groups in proteins. Their redox property of being sensitive to O2-induced oxidative damage is, for instance, used by the cell to sense oxygen levels and switch between aerobic and anaerobic metabolisms, as exemplified by the fumarate, nitrate reduction regulator (FNR). Using the hydrogenase maturase HydE from Thermotoga maritima as a template, we obtained several unusual forms of FeS clusters, some of which are associated with important structural changes. These structures represent intermediate states relevant to both FeS cluster assembly and degradation. We observe one Fe2S2 cluster bound by two cysteine persulfide residues. This observation lends structural support to a very recent Raman study, which reported that Fe4S4-to-Fe2S2 cluster conversion upon oxygen exposure in FNR resulted in concomitant production of cysteine persulfide as cluster ligands. Similar persulfide ligands have been observed in vitro for several other Fe4S4 cluster-containing proteins. We have also monitored FeS cluster conversion directly in our protein crystals. Our structures indicate that the Fe4S4-to-Fe2S2 change requires large structural modifications, which are most likely responsible for the dimer-monomer transition in FNR.


    Organizational Affiliation

    Metalloproteins Unit, Institut de Biologie Structurale J.-P. Ebel, Commissariat à l'Energie Atomique-Centre National de la Recherche Scientifique-Université Grenoble-Alpes, 38027 Grenoble, France. yvain.nicolet@ibs.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FEFE-HYDROGENASE MATURASE
A
358Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
EC: 1.8.-.-
Find proteins for Q9X0Z6 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9X0Z6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
H2S
Query on H2S

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Download CCD File 
A
HYDROSULFURIC ACID
HYDROGEN SULFIDE
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.901 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.177 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 82.430α = 90.00
b = 82.430β = 90.00
c = 217.340γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
ADSCdata collection
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-05-15
    Type: Database references