3TTV

Structure of the F413E variant of E. coli KatE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mutation of Phe413 to Tyr in catalase KatE from Escherichia coli leads to side chain damage and main chain cleavage.

Jha, V.Donald, L.J.Loewen, P.C.

(2012) Arch.Biochem.Biophys. 525: 207-214

  • DOI: 10.1016/j.abb.2011.11.022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The monofunctional catalase KatE of Esherichia coli exhibits exceptional resistance to heat denaturation and proteolytic degradation. During an investigation of subtle conformation changes in Arg111 and Phe413 on the proximal side of the heme induced ...

    The monofunctional catalase KatE of Esherichia coli exhibits exceptional resistance to heat denaturation and proteolytic degradation. During an investigation of subtle conformation changes in Arg111 and Phe413 on the proximal side of the heme induced by H(2)O(2), variants at position R111, T115 and F413 were constructed. Because the residues are not situated in the distal side heme cavity where catalysis occurs, significant changes in reactivity were not expected and indeed, only small changes in the kinetic characteristics were observed in all of the variants. However, the F413Y variant was found to have undergone main chain cleavage whereas the R111A, T115A, F413E and F413K variants had not. Two sites of cleavage were identified in the crystal structure and by mass spectrometry at residues 111 and 115. In addition to main chain cleavage, modifications to the side chains of Tyr413, Thr115 and Arg111 were suggested by differences in the electron density maps compared to maps of the native and inactive variant H128N/F413Y. The inactive variant H128N/F413Y and the active variant T115A/F413Y both did not exhibit main chain cleavage and the R11A/F413Y variant exhibited less cleavage. In addition, the apparent modification of three side chains was largely absent in these variants. It is also significant that all three F413 single variants contained heme b suggesting that the fidelity of the phenyl group was important for mediating heme b oxidation to heme d. The reactions are attributed to the introduction of a new reactive center possibly involving a transient radical on Tyr413 formed during catalytic turn over.


    Organizational Affiliation

    Department of Microbiology, University of Manitoba, Winnipeg, Canada MB R3T 2N2.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catalase HPII
A, B, C, D
753Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: katE
EC: 1.11.1.6
Find proteins for P21179 (Escherichia coli (strain K12))
Go to UniProtKB:  P21179
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
A, B, C, D
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.145 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 93.560α = 90.00
b = 133.050β = 109.29
c = 122.640γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
MxDCdata collection
REFMACphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-09-15 
  • Released Date: 2011-10-12 
  • Deposition Author(s): Loewen, P.C., Jha, V.

Revision History 

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2013-02-27
    Type: Database references