5SW6

Crystal structure of an oxoferryl species of catalase-peroxidase KatG at pH5.6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A molecular switch and electronic circuit modulate catalase activity in catalase-peroxidases.

Carpena, X.Wiseman, B.Deemagarn, T.Singh, R.Switala, J.Ivancich, A.Fita, I.Loewen, P.C.

(2005) EMBO Rep. 6: 1156-1162

  • DOI: 10.1038/sj.embor.7400550
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The catalase reaction of catalase-peroxidases involves catalase-specific features built into a peroxidase core. An arginine, 20 A from the active-site heme, acts as a molecular switch moving between two conformations, one that activates heme oxidatio ...

    The catalase reaction of catalase-peroxidases involves catalase-specific features built into a peroxidase core. An arginine, 20 A from the active-site heme, acts as a molecular switch moving between two conformations, one that activates heme oxidation and one that activates oxoferryl heme reduction by H(2)O(2), facilitating the catalatic pathway in a peroxidase. The influence of the arginine is imparted to the heme through its association with or dissociation from a tyrosinate that modulates reactivity through a Met-Tyr-Trp crosslinked adduct and a pi electron interaction of the heme with the adduct Trp.


    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-peroxidase
A, B
728Burkholderia pseudomallei (strain 1710b)Mutation(s): 0 
Gene Names: katG
EC: 1.11.1.21
Find proteins for Q3JNW6 (Burkholderia pseudomallei (strain 1710b))
Go to UniProtKB:  Q3JNW6
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A, B
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
O
Query on O

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Download CCD File 
A, B
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 100.211α = 90.00
b = 114.658β = 90.00
c = 174.378γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
AMoREphasing
REFMACrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-08-08 
  • Released Date: 2016-08-24 
  • Deposition Author(s): Loewen, P.C.
  • This entry supersedes: 2B2R

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (Canada)CanadaD9600

Revision History 

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Derived calculations, Structure summary