Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.17 kDa 
• Atom Count: 783 
• Modelled Residue Count: 100 
• Deposited Residue Count: 100 
• Unique protein chains: 1

1I6D

SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE

• PDB DOI: 10.2210/pdb1I6D/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Paracoccus denitrificans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-03-02 Released: 2001-10-17 
• Deposition Author(s): Reincke, B., Perez, C., Pristovsek, P., Luecke, C., Ludwig, C., Loehr, F., Rogov, V.V., Ludwig, B., Rueterjans, H.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: LEAST RESTRAINT VIOLATIONS 

Literature

Solution structure and dynamics of the functional domain of Paracoccus denitrificans cytochrome c(552) in both redox states.

Reincke, B., Perez, C., Pristovsek, P., Lucke, C., Ludwig, C., Lohr, F., Rogov, V.V., Ludwig, B., Ruterjans, H.

(2001) Biochemistry 40: 12312-12320

• PubMed: 11591150 
• DOI: 10.1021/bi010615o
• Primary Citation of Related Structures:  
  1I6D, 1I6E


• PubMed Abstract: 
  

A soluble and fully functional 10.5 kDa fragment of the 18.2 kDa membrane-bound cytochrome c(552) from Paracoccus denitrificans has been heterologously expressed and (13)C/(15)N-labeled to study the structural features of this protein in both redox states. Well-resolved solution structures of both the reduced and oxidized states have been determined using high-resolution heteronuclear NMR. The overall protein topology consists of two long terminal helices and three shorter helices surrounding the heme moiety. No significant redox-induced structural differences have been observed. (15)N relaxation rates and heteronuclear NOE values were determined at 500 and 600 MHz. Several residues located around the heme moiety display increased backbone mobility in both oxidation states, while helices I, III, and V as well as the two concatenated beta-turns between Leu30 and Arg36 apparently form a less flexible domain within the protein structure. Major redox-state-dependent differences of the internal backbone mobility on the picosecond-nanosecond time scale were not evident. Hydrogen exchange experiments demonstrated that the slow-exchanging amide proton resonances mainly belong to the helices and beta-turns, corresponding to the regions with high order parameters in the dynamics data. Despite this correlation, the backbone amide protons of the oxidized cytochrome c(552) exchange considerably faster with the solvent compared to the reduced protein. Using both differential scanning calorimetry as well as temperature-dependent NMR spectroscopy, a significant difference in the thermostabilities of the two redox states has been observed, with transition temperatures of 349.9 K (76.8 degrees C) for reduced and 307.5 K (34.4 degrees C) for oxidized cytochrome c(552). These results suggest a clearly distinct backbone stability between the two oxidation states.

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Related Citations: 

• Solution Structure of the Functional Domain of Paracoccus Denitrificans Cytochrome C552 in the Reduced State
  Pristovsek, P., Luecke, C., Reincke, B., Ludwig, B., Rueterjans, H.
  (2000) Eur J Biochem 267: 4205

• Structure of the Soluble Domain of Cytochrome C552 from Paracoccus Denitrificans in the Oxidized and Reduced States
  Harrenga, A., Reincke, B., Rueterjans, H., Ludwig, B., Michel, H.
  (2000) J Mol Biol 295: 667

• Heterologous Expression of Soluble Fragments of Cytochrome C552 Acting as Electron Donor to the Paracoccus Denitrificans Cytochrome C Oxidase
  Reincke, B., Thoeny-Meyer, L., Dannehl, C., Odenwald, A., Aidim, M., Witt, H., Rueterjans, H., Ludwig, B.
  (1999) Biochim Biophys Acta 1441: 114

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Organizational Affiliation: 

Institute of Biophysical Chemistry,J.W. Goethe-University of Frankfurt, Marie-Curie-Strabetae 9, 60439 Frankfurt a.M., Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C552	A	100	Paracoccus denitrificans	Mutation(s): 0  Gene Names: cycM
UniProt
Find proteins for P54820 (Paracoccus denitrificans) Explore P54820  Go to UniProtKB:  P54820

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	B [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: LEAST RESTRAINT VIOLATIONS 
• OLDERADO: 1I6D Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-03-02 
• Released Date: 2001-10-17 
Deposition Author(s): Reincke, B., Perez, C., Pristovsek, P., Luecke, C., Ludwig, C., Loehr, F., Rogov, V.V., Ludwig, B., Rueterjans, H.

Revision History  

• Version 1.0: 2001-10-17
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations