3P9S

Structure of I274A variant of E. coli KatE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Modulation of heme orientation and binding by a single residue in catalase HPII of Escherichia coli.

Jha, V.Louis, S.Chelikani, P.Carpena, X.Donald, L.J.Fita, I.Loewen, P.C.

(2011) Biochemistry 50: 2101-2110

  • DOI: 10.1021/bi200027v
  • Primary Citation of Related Structures:  3P9P, 3P9Q, 3P9R, 3PQ2, 3PQ3, 3PQ4, 3PQ5, 3PQ6, 3PQ7, 3PQ8

  • PubMed Abstract: 
  • Heme-containing catalases have been extensively studied, revealing the roles of many residues, the existence of two heme orientations, flipped 180° relative to one another along the propionate-vinyl axis, and the presence of both heme b and heme d. T ...

    Heme-containing catalases have been extensively studied, revealing the roles of many residues, the existence of two heme orientations, flipped 180° relative to one another along the propionate-vinyl axis, and the presence of both heme b and heme d. The focus of this report is a residue, situated adjacent to the vinyl groups of the heme at the entrance of the lateral channel, with an unusual main chain geometry that is conserved in all catalase structures so far determined. In Escherichia coli catalase HPII, the residue is Ile274, and replacing it with Gly, Ala, and Val, found at the same location in other catalases, results in a reduction in catalytic efficiency, a reduced intensity of the Soret absorbance band, and a mixture of heme orientations and species. The reduced turnover rates and higher H(2)O(2) concentrations required to attain equivalent reaction velocities are explained in terms of less efficient containment of substrate H(2)O(2) in the heme cavity arising from easier escape through the more open entrance to the lateral channel created by the smaller side chains of Gly and Ala. Inserting a Cys at position 274 resulted in the heme being covalently linked to the protein through a Cys-vinyl bond that is hypersensitive to X-ray irradiation being largely degraded within seconds of exposure to the X-ray beam. Two heme orientations, flipped along the propionate-vinyl axis, are found in the Ala, Val, and Cys variants.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catalase HPII
A, B, C, D
753Escherichia coli (strain K12)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
HDE
Query on HDE

Download SDF File 
Download CCD File 
A, B, C, D
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE 17R, 18S
C34 H38 Fe N4 O5
SQSYUADQFVTXKU-CAMYIWQSSA-N
 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: 1.9 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.137 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 93.560α = 90.00
b = 133.170β = 109.24
c = 122.810γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
PDB_EXTRACTdata extraction
MxDCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-07-27
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description