3HQ6

Cytochrome c peroxidase from G. sulfurreducens, wild type


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

CcpA from Geobacter sulfurreducens is a basic di-heme cytochrome c peroxidase.

Hoffmann, M.Seidel, J.Einsle, O.

(2009) J Mol Biol 393: 951-965

  • DOI: https://doi.org/10.1016/j.jmb.2009.09.001
  • Primary Citation of Related Structures:  
    3HQ6, 3HQ7, 3HQ8, 3HQ9

  • PubMed Abstract: 

    Bacterial di-heme cytochrome c peroxidases (CcpAs) protect the cell from reactive oxygen species by reducing hydrogen peroxide to water. The enzymes are c-type cytochromes, with both heme groups covalently attached to the protein chain via a characteristic binding motif. The genome of the dissimilatory metal-reducing bacterium Geobacter sulfurreducens revealed the presence of a ccpA gene and we isolated the gene product after recombinant expression in Escherichia coli. CcpA from G. sulfurreducens exhibited in vitro peroxidase activity with ABTS(2-) [2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid)] as an electron donor, and the three-dimensional structure of the dimeric enzyme has been determined to high resolution. For activation, CcpA commonly requires reduction, with the exception of the Nitrosomonas europaea enzyme that retains its activity in the oxidized state. A G94K/K97Q/R100I triple point mutant was created to mimic the critical loop region of N. europaea CcpA, but its crystal structure revealed that the inactive, bis-histidinyl-coordinated form of the active-site heme group was retained. Subsequent mutational studies thus addressed an adjacent loop region, where a change in secondary structure accompanies the reductive activation of the enzyme. While an A124K/K128A double mutant did not show significant changes, the CcpA variants S134P/V135K and S134P led to a distortion of the loop region, accompanied by an opening of the active-site loop, leaving the enzyme in a constitutively active state.


  • Organizational Affiliation

    Lehrstuhl für Biochemie, Institut für organische Chemie und Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, Freiburg 79104, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c551 peroxidase
A, B
345Geobacter sulfurreducensMutation(s): 0 
Gene Names: ccpAccpA-2GSU2813
EC: 1.11.1.5
UniProt
Find proteins for Q749D0 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
Explore Q749D0 
Go to UniProtKB:  Q749D0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ749D0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.241α = 68.69
b = 55.783β = 71.84
c = 78.644γ = 57.76
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description