4ENS

Structure of E530Q variant of E. coli KatE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Influence of main channel structure on H(2)O(2) access to the heme cavity of catalase KatE of Escherichia coli.

Jha, V.Chelikani, P.Carpena, X.Fita, I.Loewen, P.C.

(2012) Arch.Biochem.Biophys. 526: 54-59

  • DOI: 10.1016/j.abb.2012.06.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The main channel for H(2)O(2) access to the heme cavity in large subunit catalases is twice as long as in small subunit catalases and is divided into two distinct parts. Like small subunit catalases, the 15Å of the channel adjacent to the heme has a ...

    The main channel for H(2)O(2) access to the heme cavity in large subunit catalases is twice as long as in small subunit catalases and is divided into two distinct parts. Like small subunit catalases, the 15Å of the channel adjacent to the heme has a predominantly hydrophobic surface with only weak water occupancy, but the next 15Å extending to the protein surface is hydrophilic and contains a complex water matrix in multiple passages. At the approximate junction of these two sections are a conserved serine and glutamate that are hydrogen bonded and associated with H(2)O(2) in inactive variants. Mutation of these residues changed the dimensions of the channel, both enlarging and constricting it, and also changed the solvent occupancy in the hydrophobic, inner section of the main channel. Despite these structural changes and the prominent location of the residues in the channel, the variants exhibited less than a 2-fold change in the k(cat) and apparent K(M) kinetic constants. These results reflect the importance of the complex multi-passage structure of the main channel. Surprisingly, mutation of either the serine or glutamate to an aliphatic side chain interfered with heme oxidation to heme d.


    Organizational Affiliation

    Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Download SDF File 
Download CCD File 
A, B, C, D
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
HEME
C34 H32 Fe N4 O5
UMGOPAWIGKFTRK-QQDQPIDJSA-N
 Ligand Interaction
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 93.450α = 90.00
b = 133.400β = 109.18
c = 123.240γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-04-13 
  • Released Date: 2012-05-02 
  • Deposition Author(s): Loewen, P.C., Jha, V.

Revision History 

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2013-02-27
    Type: Database references