Structure of the mutant VAL169CYS of catalase HPII from Escherichia coli

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.181 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


Mutants that alter the covalent structure of catalase hydroperoxidase II from Escherichia coli.

Mate, M.J.Sevinc, M.S.Hu, B.Bujons, J.Bravo, J.Switala, J.Ens, W.Loewen, P.C.Fita, I.

(1999) J Biol Chem 274: 27717-27725

  • DOI: https://doi.org/10.1074/jbc.274.39.27717
  • Primary Citation of Related Structures:  
    1CF9, 1QF7

  • PubMed Abstract: 

    The three-dimensional structures of two HPII variants, V169C and H392Q, have been determined at resolutions of 1.8 and 2.1 A, respectively. The V169C variant contains a new type of covalent bond between the sulfur atom of Cys(169) and a carbon atom on the imidazole ring of the essential His(128). This variant enzyme has only residual catalytic activity and contains heme b. The chain of water molecules visible in the main channel may reflect the organization of the hydrogen peroxide substrates in the active enzyme. Two alternative mechanisms, involving either compound I or free radical intermediates, are presented to explain the formation of the Cys-His covalent bond. The H392Q and H392E variants exhibit 75 and 25% of native catalytic activity, respectively. The Gln(392) variant contains only heme b, whereas the Glu(392) variant contains a mixture of heme b and cis and trans isomers of heme d, suggesting of a role for this residue in heme conversion. Replacement of either Gln(419) and Ser(414), both of which interact with the heme, affected the cis:trans ratio of spirolactone heme d. Implications for the heme oxidation mechanism and the His-Tyr bond formation in HPII are considered.

  • Organizational Affiliation

    CID (Consejo Superior de Investigaciones Cietifícas) Jordi Girona 18-26, 08034 Barcelona, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
753Escherichia coliMutation(s): 1 
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: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.47α = 90
b = 133.04β = 109.64
c = 122.22γ = 90
Software Package:
Software NamePurpose
CCP4model building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-04-06
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2014-03-12
    Changes: Database references, Structure summary
  • Version 1.4: 2018-03-14
    Changes: Data collection, Database references
  • Version 1.5: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description