3HQ9

CcpA from G. sulfurreducens, S134P variant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c551 peroxidase A, B345Geobacter sulfurreducensMutation(s): 1 
Gene Names: ccpA, ccpA-2, GSU2813
EC: 1.11.1.5
Find proteins for Q749D0 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
Explore Q749D0 
Go to UniProtKB:  Q749D0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
BU3
Query on BU3
Download Ideal Coordinates CCD File 
A, B
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N		 Ligand Interaction
OXL
Query on OXL
Download Ideal Coordinates CCD File 
A, B
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L		 Ligand Interaction
IMD
Query on IMD
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A, B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O		 Ligand Interaction
CA
Query on CA
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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.899α = 104.71
b = 55.473β = 99.39
c = 68.606γ = 108.97
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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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: Advisory, Refinement description, Version format compliance