Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

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Crystal structure of catalase HPII from Escherichia coli.

Bravo, J.Verdaguer, N.Tormo, J.Betzel, C.Switala, J.Loewen, P.C.Fita, I.

(1995) Structure 3: 491-502

  • DOI: https://doi.org/10.1016/s0969-2126(01)00182-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Catalase is a ubiquitous enzyme present in both the prokaryotic and eukaryotic cells of aerobic organisms. It serves, in part, to protect the cell from the toxic effects of small peroxides. Escherichia coli produces two catalases, HPI and HPII, that are quite distinct from other catalases in physical structure and catalytic properties. HPII, studied in this work, is encoded by the katE gene, and has been characterized as an oligomeric, monofunctional catalase containing one cis-heme d prosthetic group per subunit of 753 residues. The crystal structure of catalase HPII from E. coli has been determined to 2.8 A resolution. The asymmetric unit of the crystal contains a whole molecule, which is a tetramer with accurate 222 point group symmetry. In the model built, that includes residues 27-753 and one heme group per monomer, strict non-crystallographic symmetry has been maintained. The crystallographic agreement R-factor is 20.1% for 58,477 reflections in the resolution shell 8.0-2.8 A. Despite differences in size and chemical properties, which were suggestive of a unique catalase, the deduced structure of HPII is related to the structure of catalase from Penicillium vitale, whose sequence is not yet known. In particular, both molecules have an additional C-terminal domain that is absent in the bovine catalase. This extra domain contains a Rossmann fold but no bound nucleotides have been detected, and its physiological role is unknown. In HPII, the heme group is modified to a heme d and inverted with respect to the orientation determined in all previously reported heme catalases. HPII is the largest catalase for which the structure has been determined to almost atomic resolution.

  • Organizational Affiliation

    Departamento de Ingeniería Química, Universidad Politécnica de Catalunña, Barcelona, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
753Escherichia coliMutation(s): 0 
Find proteins for P21179 (Escherichia coli (strain K12))
Explore P21179 
Go to UniProtKB:  P21179
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21179
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.2α = 90
b = 134.7β = 109.4
c = 124.4γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-09-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-05-31
    Changes: Database references, Derived calculations, Other
  • Version 2.0: 2023-09-27
    Type: Remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description