1I6D

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • Primary Citation of Related Structures:  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 s ...

    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.


    Related Citations: 
    • 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
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C552
A
100Paracoccus denitrificansGene Names: cycM
Find proteins for P54820 (Paracoccus denitrificans)
Go to UniProtKB:  P54820
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download SDF File 
Download CCD File 
A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance