1CF9

Structure of the mutant VAL169CYS of catalase HPII from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

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

  • Primary Citation of Related Structures:  

  • 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 o ...

    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: 
    • 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
    • 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.,Sect.A 28: 79
    • 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.,Sect.B 42: 497


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CATALASE HPII)
A, B, C, D
753Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: katE
EC: 1.11.1.6
Find proteins for P21179 (Escherichia coli (strain K12))
Go to UniProtKB:  P21179
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 93.470α = 90.00
b = 133.040β = 109.64
c = 122.220γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CCP4model building
CCP4phasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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