4O5Q

Crystal Structure of the Alkylhydroperoxide Reductase AhpF from Escherichia coli

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.144 

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This is version 1.2 of the entry. See complete history. 


Literature

Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF from Escherichia coli

Dip, P.V., Kamariah, N., Subramanian Manimekalai, M.S., Nartey, W., Balakrishna, A.M., Eisenhaber, F., Eisenhaber, B., Gruber, G.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2848-2862

  • DOI: 10.1107/S1399004714019233
  • Primary Citation of Related Structures:  
    4O5Q, 4O5R, 4O5U

  • PubMed Abstract: 

    • Hydroperoxides are reactive oxygen species (ROS) that are toxic to all cells and must be converted into the corresponding alcohols to alleviate oxidative stress. In Escherichia coli, the enzyme primarily responsible for this reaction is alkylhydroperoxide reductase (AhpR) ...

    Hydroperoxides are reactive oxygen species (ROS) that are toxic to all cells and must be converted into the corresponding alcohols to alleviate oxidative stress. In Escherichia coli, the enzyme primarily responsible for this reaction is alkylhydroperoxide reductase (AhpR). Here, the crystal structures of both of the subunits of EcAhpR, EcAhpF (57 kDa) and EcAhpC (21 kDa), have been solved. The EcAhpF structures (2.0 and 2.65 Å resolution) reveal an open and elongated conformation, while that of EcAhpC (3.3 Å resolution) forms a decameric ring. Solution X-ray scattering analysis of EcAhpF unravels the flexibility of its N-terminal domain, and its binding to EcAhpC was demonstrated by isothermal titration calorimetry. These studies suggest a novel overall mechanistic model of AhpR as a hydroperoxide scavenger, in which the dimeric, extended AhpF prefers complex formation with the AhpC ring to accelerate the catalytic activity and thus to increase the chance of rescuing the cell from ROS.

    Related Citations: 
    • Crystal structure of the catalytic core component of the alkylhydroperoxide reductase AhpF from Escherichia coli
      Bieger, B., Essen, L.O.
      (2010) J Mol Biol 307: 1
    • Structure of intact AhpF reveals a mirrored thioredoxin-like active site and implies large domain rotations during catalysis
      Wood, Z.A., Poole, L.B., Karplus, P.A.
      (2001) Biochemistry 40: 3900
    Organizational Affiliation: 

    School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alkyl hydroperoxide reductase subunit FA521Escherichia coli K-12Mutation(s): 0 
Gene Names: ahpF, b0606, JW0599
EC: 1.8.1
UniProt
Find proteins for P35340 (Escherichia coli (strain K12))
Explore P35340 
Go to UniProtKB:  P35340
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35340
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
PG4
Query on PG4
Download Ideal Coordinates CCD File 
R [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N		 Ligand Interaction
PGE
Query on PGE
Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
M [auth A],
Q [auth A],
S [auth A],
K [auth A],
L [auth A],
M [auth A],
Q [auth A],
S [auth A],
V [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N		 Ligand Interaction
TRS
Query on TRS
Download Ideal Coordinates CCD File 
U [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
CD
Query on CD
Download Ideal Coordinates CCD File 
O [auth A]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
N [auth A],
P [auth A],
T [auth A],
W [auth A],
X [auth A],
N [auth A],
P [auth A],
T [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.144 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.494α = 90
b = 58.696β = 114.58
c = 123.994γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Database references
  • Version 1.2: 2015-02-25
    Changes: Database references