Atomic resolution structure of Micrococcus Lysodeikticus catalase

Experimental Data Snapshot

  • Resolution: 0.88 Å
  • R-Value Free: 0.096 
  • R-Value Work: 0.089 
  • R-Value Observed: 0.089 

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The Structures of Micrococcus Lysodeikticus Catalase, its Ferryl Intermediate (Compound II) and Nadph Complex.

Murshudov, G.N.Grebenko, A.I.Brannigan, J.A.Antson, A.A.Barynin, V.V.Dodson, G.G.Dauter, Z.Wilson, K.S.Melik-Adamyan, W.R.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1972-1982

  • DOI: https://doi.org/10.1107/s0907444902016566
  • Primary Citation of Related Structures:  
    1GWE, 1GWF, 1GWH

  • PubMed Abstract: 

    The crystal structure of the bacterial catalase from Micrococcus lysodeikticus has been refined using the gene-derived sequence both at 0.88 A resolution using data recorded at 110 K and at 1.5 A resolution with room-temperature data. The atomic resolution structure has been refined with individual anisotropic atomic thermal parameters. This has revealed the geometry of the haem and surrounding protein, including many of the H atoms, with unprecedented accuracy and has characterized functionally important hydrogen-bond interactions in the active site. The positions of the H atoms are consistent with the enzymatic mechanism previously suggested for beef liver catalase. The structure reveals that a 25 A long channel leading to the haem is filled by partially occupied water molecules, suggesting an inherent facile access to the active site. In addition, the structures of the ferryl intermediate of the catalase, the so-called compound II, at 1.96 A resolution and the catalase complex with NADPH at 1.83 A resolution have been determined. Comparison of compound II and the resting state of the enzyme shows that the binding of the O atom to the iron (bond length 1.87 A) is associated with increased haem bending and is accompanied by a distal movement of the iron and the side chain of the proximal tyrosine. Finally, the structure of the NADPH complex shows that the cofactor is bound to the molecule in an equivalent position to that found in beef liver catalase, but that only the adenine part of NADPH is visible in the present structure.

  • Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England. garib@ysbl.york.ac.uk

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catalase503Micrococcus luteusMutation(s): 0 
Find proteins for P29422 (Micrococcus luteus)
Explore P29422 
Go to UniProtKB:  P29422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29422
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 0.88 Å
  • R-Value Free: 0.096 
  • R-Value Work: 0.089 
  • R-Value Observed: 0.089 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.785α = 90
b = 105.785β = 90
c = 105.001γ = 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: 2002-04-26
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2018-06-20
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.3: 2019-07-10
    Changes: Data collection
  • Version 1.4: 2019-07-24
    Changes: Data collection
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other