Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 77.24 kDa 
• Atom Count: 5448 
• Modelled Residue Count: 618 
• Deposited Residue Count: 690 
• Unique protein chains: 1

3HQ9

CcpA from G. sulfurreducens, S134P variant

• PDB DOI: 10.2210/pdb3HQ9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Geobacter sulfurreducens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-06-05 Released: 2009-09-22 
• Deposition Author(s): Hoffmann, M., Seidel, J., Einsle, O.

---

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 

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

• PubMed: 19735665 
• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c551 peroxidase	A, B	345	Geobacter sulfurreducens	Mutation(s): 1  Gene Names: ccpA, ccpA-2, GSU2813 EC: 1.11.1.5
UniProt
Find proteins for Q749D0 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q749D0  Go to UniProtKB:  Q749D0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth A], K [auth B], L [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BU3	J [auth A], R [auth B]	(R,R)-2,3-BUTANEDIOL C4 H10 O2 OWBTYPJTUOEWEK-QWWZWVQMSA-N
OXL	H [auth A], I [auth A], P [auth B], Q [auth B]	OXALATE ION C2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-L
IMD	F [auth A], G [auth A], N [auth B], O [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CA	E [auth A], M [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 50.899	α = 104.71
b = 55.473	β = 99.39
c = 68.606	γ = 108.97

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-06-05 
• Released Date: 2009-09-22 
Deposition Author(s): Hoffmann, M., Seidel, J., Einsle, O.

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2021-10-13
  Changes: Data collection, Database references, Derived calculations