1CF9

Structure of the mutant VAL169CYS of catalase HPII from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.181 

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Literature

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) ...

    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.


    Related Citations: 
    • 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
    • 2.8 A Crystal Structure of Catalase Hpii from Escherichia Coli
      Bravo, J., Tormo, J., Verdaguer, N., Fita, I., Betzel, C., Switala, J., Loewen, P.C.
      (1993) Acta Crystallogr A 28: 79
    • Crystallization and Preliminary X-Ray Diffraction Analysis of Catalase Hpii from Escherichia Coli
      Tormo, J., Fita, I., Switala, J., Loewen, P.C.
      (1990) J Mol Biol 213: 219
    • The Refined Structure of Beef Liver Catalase at 2.5 A Resolution
      Fita, I., Silva, A.M., Murthy, M.R.N., Rossmann, M.G.
      (1986) Acta Crystallogr B 42: 497

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (CATALASE HPII)A, B, C, D753Escherichia coliMutation(s): 1 
EC: 1.11.1.6
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

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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