High resolution Zn containing Iron sulfur cluster repair protein YtfE

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal Structure of the Repair of Iron Centers Protein Ytfe and its Interaction with No

Lo, F.-C.Hsieh, C.-C.Maestre-Reyna, M.Chen, C.-Y.Ko, T.-P.Horng, Y.-C.Lai, Y.-C.Chiang, Y.-W.Chou, C.-M.Chiang, C.-H.Huang, W.-N.Liaw, W.-F.

(2016) Chemistry 22: 9768

  • DOI: https://doi.org/10.1002/chem.201600990
  • Primary Citation of Related Structures:  
    5FNN, 5FNP, 5FNY

  • PubMed Abstract: 

    Molecular mechanisms underlying the repair of nitrosylated [Fe-S] clusters by the microbial protein YtfE remain poorly understood. The X-ray crystal structure of YtfE, in combination with EPR, magnetic circular dichroism (MCD), UV, and (17) O-labeling electron spin echo envelope modulation measurements, show that each iron of the oxo-bridged Fe(II) -Fe(III) diiron core is coordinatively unsaturated with each iron bound to two bridging carboxylates and two terminal histidines in addition to an oxo-bridge. Structural analysis reveals that there are two solvent-accessible tunnels, both of which converge to the diiron center and are critical for capturing substrates. The reactivity of the reduced-form Fe(II) -Fe(II) YtfE toward nitric oxide demonstrates that the prerequisite for N2 O production requires the two iron sites to be nitrosylated simultaneously. Specifically, the nitrosylation of the two iron sites prior to their reductive coupling to produce N2 O is cooperative. This result suggests that, in addition to any repair of iron centers (RIC) activity, YtfE acts as an NO-trapping scavenger to promote the NO to N2 O transformation under low NO flux, which precedes nitrosative stress.

  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
220Escherichia coli K-12Mutation(s): 2 
Gene Names: ytfEb4209JW4167
Find proteins for P69506 (Escherichia coli (strain K12))
Explore P69506 
Go to UniProtKB:  P69506
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69506
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.454α = 90
b = 98.454β = 90
c = 126.138γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-06-15
    Changes: Database references
  • Version 1.2: 2016-07-13
    Changes: Database references