5B8A

Crystal structure of oxidized chimeric EcAhpC1-186-YFSKHN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Transition steps in peroxide reduction and a molecular switch for peroxide robustness of prokaryotic peroxiredoxins.

Kamariah, N.Sek, M.F.Eisenhaber, B.Eisenhaber, F.Gruber, G.

(2016) Sci Rep 6: 37610-37610

  • DOI: 10.1038/srep37610
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In addition to their antioxidant function, the eukaryotic peroxiredoxins (Prxs) facilitate peroxide-mediated signaling by undergoing controlled inactivation by peroxide-driven over-oxidation. In general, the bacterial enzyme lacks this controlled ina ...

    In addition to their antioxidant function, the eukaryotic peroxiredoxins (Prxs) facilitate peroxide-mediated signaling by undergoing controlled inactivation by peroxide-driven over-oxidation. In general, the bacterial enzyme lacks this controlled inactivation mechanism, making it more resistant to high H2O2 concentrations. During peroxide reduction, the active site alternates between reduced, fully folded (FF), and oxidized, locally unfolded (LU) conformations. Here we present novel insights into the divergence of bacterial and human Prxs in robustness and sensitivity to inactivation, respectively. Structural details provide new insights into sub-steps during the catalysis of peroxide reduction, enabling the transition from an FF to a LU conformation. Complementary to mutational and enzymatic results, these data unravel the essential role of the C-terminal tail of bacterial Prxs to act as a molecular switch, mediating the transition from an FF to a LU state. In addition, we propose that the C-terminal tail has influence on the propensity of the disulphide bond formation, indicating that as a consequence on the robustness and sensitivity to over-oxidation. Finally, a physical linkage between the catalytic site, the C-terminal tail and the oligomer interface is described.


    Related Citations: 
    • The ups and downs in AhpF: Structure, mechanism and ensemble formation of the Alkylhydroperoxide Reductase subunits AhpC and AhpF from Escherichia coli
      Dip, P.V.,Kamariah, N.,Manimekalai, M.S.S.,Nartey, W.,Balakrishna, A.M.,Eisenhaber, F.,Eisenhaber, B.,Gruber, G.
      (2014) Acta Cryst D 70: 2848


    Organizational Affiliation

    Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
A, B, C, D, E, F, G, H, I, J
192Homo sapiensEscherichia coli (strain K12)
This entity is chimeric
Mutation(s): 0 
Gene Names: PRDX2 (NKEFB, TDPX1), ahpC
EC: 1.11.1.15 1.11.1.15
Find proteins for P32119 (Homo sapiens)
Go to Gene View: PRDX2
Go to UniProtKB:  P32119
Find proteins for P0AE08 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AE08
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, D, E, F, G, H, J
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.244 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 99.470α = 90.00
b = 134.730β = 111.06
c = 107.530γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-01
    Type: Initial release