1FOC

Cytochrome C557: improperly folded thermus thermophilus C552


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.423 
  • R-Value Work: 0.273 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Recombinant cytochrome rC557 obtained from Escherichia coli cells expressing a truncated Thermus thermophilus cycA gene. Heme inversion in an improperly matured protein

McRee, D.E.Williams, P.A.Sridhar, V.Pastuszyn, A.Bren, K.L.Chen, Y.Patel, K.M.Todaro, T.R.Sanders, D.Luna, E.Fee, J.A.

(2001) J.Biol.Chem. 276: 6537-6544

  • DOI: 10.1074/jbc.M008421200

  • PubMed Abstract: 
  • Cytochrome rC(557) is an improperly matured, dimeric cytochrome c obtained from expression of the "signal peptide-lacking" Thermus thermophilus cycA gene in the cytoplasm of Escherichia coli. It is characterized by its Q(00) (or alpha-) optical absor ...

    Cytochrome rC(557) is an improperly matured, dimeric cytochrome c obtained from expression of the "signal peptide-lacking" Thermus thermophilus cycA gene in the cytoplasm of Escherichia coli. It is characterized by its Q(00) (or alpha-) optical absorption band at 557 nm in the reduced form (Keightley, J. A., Sanders, D., Todaro, T. R., Pastuszyn, A., and Fee, J. A. (1998) J. Biol. Chem. 273, 12006-12016). We report results of a broad ranging, biochemical and spectral characterization of this protein that reveals the presence of a free vinyl group on the porphyrin and a disulfide bond between the protomers and supports His-Met ligation in both valence states of the iron. A 3-A resolution x-ray structure shows that, in comparison with the native protein, the heme moiety is rotated 180 degrees about its alpha,gamma-axis; cysteine 14 has formed a thioether bond with the 2-vinyl of pyrrole ring I instead of the 4-vinyl of pyrrole ring II, as occurs in the native protein; and a cysteine 11 from each protomer has formed an intermolecular disulfide bond. Numerous, minor perturbations exist within the structure of rC(557) in comparison with that of native protein, which result from heme inversion and protein-protein interactions across the dimer interface. The unusual spectral properties of rC(557) are rationalized in terms of this structure.


    Related Citations: 
    • Integrity of thermus thermophilus cytochrome C552 synthesized by Escherichia coli cells expressing the host-specific cytochrome C maturation genes, CCMABCDEFGH: biochemical, spectral and structural characterization of the recombinant protein
      Sridhar, V.,Pastuszyn, A.,Patel, K.M.,Chen, Y.,Todaro, T.R.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Molecular Biology, the Scripps Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME RC557
A, B
132Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: cycA
Find proteins for Q5SME3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SME3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.423 
  • R-Value Work: 0.273 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.720α = 90.00
b = 69.050β = 90.00
c = 36.582γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
CNSrefinement
XTALVIEWrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2018-01-31
    Type: Advisory, Experimental preparation