5B8A

Crystal structure of oxidized chimeric EcAhpC1-186-YFSKHN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1038/srep37610
  • Primary Citation of Related Structures:  
    5B8A, 5B8B

  • 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 inactivation mechanism, making it more resistant to high H 2 O 2 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
192Escherichia coli K-12Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: ahpCb0605JW0598PRDX2NKEFBTDPX1
EC: 1.11.1.15 (PDB Primary Data), 1.11.1.26 (UniProt), 1.11.1.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P32119 (Homo sapiens)
Explore P32119 
Go to UniProtKB:  P32119
PHAROS:  P32119
GTEx:  ENSG00000167815 
Find proteins for P0AE08 (Escherichia coli (strain K12))
Explore P0AE08 
Go to UniProtKB:  P0AE08
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AE08P32119
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
DA [auth E]
HA [auth F]
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth E],
HA [auth F],
IA [auth F],
K [auth A],
KA [auth G],
L [auth A],
LA [auth G],
M [auth A],
P [auth B],
PA [auth H],
Q [auth B],
QA [auth H],
R [auth B],
TA [auth I],
U [auth C],
UA [auth I],
V [auth D],
VA [auth J],
W [auth D],
WA [auth J]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth J]
BB [auth J]
CB [auth J]
EA [auth E]
FA [auth E]
AB [auth J],
BB [auth J],
CB [auth J],
EA [auth E],
FA [auth E],
GA [auth E],
JA [auth F],
MA [auth G],
N [auth A],
NA [auth G],
O [auth A],
OA [auth G],
RA [auth H],
S [auth B],
SA [auth H],
T [auth B],
X [auth D],
XA [auth J],
Y [auth D],
YA [auth J],
Z [auth D],
ZA [auth J]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.47α = 90
b = 134.73β = 111.06
c = 107.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary