Crystal Structure Analysis of Catalase CatF of Pseudomonas syringae

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.183 

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Structure of the Clade 1 catalase, CatF of Pseudomonas syringae, at 1.8 A resolution

Carpena, X.Soriano, M.Klotz, M.G.Duckworth, H.W.Donald, L.J.Melik-Adamyan, W.Fita, I.Loewen, P.C.

(2003) Proteins 50: 423-436

  • DOI: https://doi.org/10.1002/prot.10284
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Catalase CatF of Pseudomonas syringae has been identified phylogenetically as a clade 1 catalase, closely related to plant catalases, a group from which no structure has been determined. The structure of CatF has been refined at 1.8 A resolution by using X-ray synchrotron data collected from a crystal flash-cooled with liquid nitrogen. The crystallographic agreement factors R and R(free) are, respectively, 18.3% and 24.0%. The asymmetric unit of the crystal contains a whole molecule that shows accurate 222-point group symmetry. The crystallized enzyme is a homotetramer of subunits with 484 residues, some 26 residues shorter than predicted from the DNA sequence. Mass spectrometry analysis confirmed the absence of 26 N-terminal residues, possibly removed by a periplasmic transport system. The core structure of the CatF subunit was closely related to seven other catalases with root-mean-square deviations (RMSDs) of 368 core Calpha atoms of 0.99-1.30 A. The heme component of CatF is heme b in the same orientation that is found in Escherichia coli hydroperoxidase II, an orientation that is flipped 180 degrees with respect the orientation of the heme in bovine liver catalase. NADPH is not found in the structure of CatF because key residues required for nucleotide binding are missing; 2129 water molecules were refined into the model. Water occupancy in the main or perpendicular channel of CatF varied among the four subunits from two to five in the region between the heme and the conserved Asp150. A comparison of the water occupancy in this region with the same region in other catalases reveals significant differences among the catalases.

  • Organizational Affiliation

    CID-CSIC, Jordi-Girona 18-26, Barcelona, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
484Pseudomonas syringaeMutation(s): 0 
Gene Names: CATF
Find proteins for P46206 (Pseudomonas syringae pv. syringae)
Explore P46206 
Go to UniProtKB:  P46206
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46206
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.63α = 90
b = 153.87β = 102.8
c = 109.19γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-28
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations