1A4E

CATALASE A FROM SACCHAROMYCES CEREVISIAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of catalase-A from Saccharomyces cerevisiae.

Mate, M.J.Zamocky, M.Nykyri, L.M.Herzog, C.Alzari, P.M.Betzel, C.Koller, F.Fita, I.

(1999) J Mol Biol 286: 135-149

  • DOI: 10.1006/jmbi.1998.2453
  • Primary Citation of Related Structures:  
    1A4E

  • PubMed Abstract: 
  • The structure of the peroxisomal catalase A from the budding yeast Saccharomyces cerevisiae, with 515 residues per subunit, has been determined and refined to 2.4 A resolution. The crystallographic agreement factors R and Rfree are 15.4% and 19.8%, respectively ...

    The structure of the peroxisomal catalase A from the budding yeast Saccharomyces cerevisiae, with 515 residues per subunit, has been determined and refined to 2.4 A resolution. The crystallographic agreement factors R and Rfree are 15.4% and 19.8%, respectively. A tetramer with accurate 222-molecular symmetry is located in the asymmetric unit of the crystal. The conformation of the central core of catalase A, about 300 residues, remains similar to the structure of catalases from distantly related organisms. In contrast, catalase A lacks a carboxy-terminal domain equivalent to that found in catalase from Penicillium vitalae, the only other fungal catalase structure available. Structural peculiarities related with the heme and NADP(H) binding pockets can be correlated with biochemical characteristics of the catalase A enzyme. The network of molecular cavities and channels, filled with solvent molecules, supports the existence of one major substrate entry and at least two possible alternative pathways to the heme active site. The structure of the variant protein Val111Ala, also determined by X-ray crystallography at 2.8 A resolution, shows a few, well-localized, differences with respect to the wild-type enzyme. These differences, that include the widening of the entry channel in its narrowest point, provide an explanation for both the increased peroxidatic activity and the reduced catalatic activity of this mutant.


    Organizational Affiliation

    CID, Jordi-Girona 18-26, Barcelona, 08034, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CATALASE AA, B, C, D488Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.11.1.6
UniProt
Find proteins for P15202 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P15202 
Go to UniProtKB:  P15202
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15202
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.172α = 90
b = 184.172β = 90
c = 304.977γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 1999-08-13 
  • Deposition Author(s): Mate, M.J.

Revision History  (Full details and data files)

  • Version 1.0: 1999-08-13
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance