4AUM

Crystal structure, recombinant expression and mutagenesis studies of the bifunctional catalase-phenol oxidase from Scytalidium thermophilum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 

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Ligand Structure Quality Assessment 


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Literature

Structure, Recombinant Expression and Mutagenesis Studies of the Catalase with Oxidase Activity from Scytalidium Thermophilum

Yuzugullu, Y.Trinh, C.H.Smith, M.A.Pearson, A.R.Phillips, S.E.V.Sutay Kocabas, D.Bakir, U.Ogel, Z.B.McPherson, M.J.

(2013) Acta Crystallogr D Biol Crystallogr 69: 398

  • DOI: 10.1107/S0907444912049001
  • Primary Citation of Related Structures:  
    4AUE, 4AUL, 4AUM, 4AUN

  • PubMed Abstract: 
  • Scytalidium thermophilum produces a catalase with phenol oxidase activity (CATPO) that catalyses the decomposition of hydrogen peroxide into oxygen and water and also oxidizes various phenolic compounds. A codon-optimized catpo gene was cloned and expressed in Escherichia coli ...

    Scytalidium thermophilum produces a catalase with phenol oxidase activity (CATPO) that catalyses the decomposition of hydrogen peroxide into oxygen and water and also oxidizes various phenolic compounds. A codon-optimized catpo gene was cloned and expressed in Escherichia coli. The crystal structures of native and recombinant S. thermophilum CATPO and two variants, H82N and V123F, were determined at resolutions of 2.7, 1.4, 1.5 and 1.9 Å, respectively. The structure of CATPO reveals a homotetramer with 698 residues per subunit and with strong structural similarity to Penicillium vitale catalase. The haem component is cis-hydroxychlorin γ-spirolactone, which is rotated 180° with respect to small-subunit catalases. The haem-binding pocket contains two highly conserved water molecules on the distal side. The H82N mutation resulted in conversion of the native d-type haem to a b-type haem. Kinetic studies of the H82N and V123F mutants indicate that both activities are likely to be associated with the haem centre and suggest that the secondary oxidase activity may be a general feature of catalases in the absence of hydrogen peroxide.


    Organizational Affiliation

    Department of Biology, Kocaeli University, 41380 Kocaeli, Turkey.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CATALASE-PHENOL OXIDASEA, B, C, D719Mycothermus thermophilusMutation(s): 0 
EC: 1.11.1.6
UniProt
Find proteins for M4GGR7 (Mycothermus thermophilus)
Explore M4GGR7 
Go to UniProtKB:  M4GGR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM4GGR7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HDD
Query on HDD

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
N [auth C],
Q [auth D]
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
C34 H32 Fe N4 O5
UMGOPAWIGKFTRK-QQDQPIDJSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
G [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
F [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
R [auth D],
S [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 201.42α = 90
b = 121.447β = 115.51
c = 125.208γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-04-03
    Changes: Database references