2EXV

Crystal structure of the F7A mutant of the cytochrome c551 from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Unveiling a Hidden Folding Intermediate in c-Type Cytochromes by Protein Engineering

Borgia, A.Bonivento, D.Travaglini-Allocatelli, C.Di Matteo, A.Brunori, M.

(2006) J.Biol.Chem. 281: 9331-9336

  • DOI: 10.1074/jbc.M512127200

  • PubMed Abstract: 
  • Several investigators have highlighted a correlation between the basic features of the folding process of a protein and its topology, which dictates the folding pathway. Within this conceptual framework we proposed that different members of the cytoc ...

    Several investigators have highlighted a correlation between the basic features of the folding process of a protein and its topology, which dictates the folding pathway. Within this conceptual framework we proposed that different members of the cytochrome c (cyt c) family share the same folding mechanism, involving a consensus partially structured state. Pseudomonas aeruginosa cyt c(551) (Pa cyt c(551)) folds via an apparent two-state mechanism through a high energy intermediate. Here we present kinetic evidence demonstrating that it is possible to switch its folding mechanism from two to three state, stabilizing the high energy intermediate by rational mutagenesis. Characterization of the folding kinetics of one single-site mutant of the Pa cyt c(551) (Phe(7) to Ala) indeed reveals an additional refolding phase and a fast unfolding process which are explained by the accumulation of a partially folded species. Further kinetic analysis highlights the presence of two parallel processes both leading to the native state, suggesting that the above mentioned species is a non obligatory on-pathway intermediate. Determination of the crystallographic structure of F7A shows the presence of an extended internal cavity, which hosts three "bound" water molecules and a H-bond in the N-terminal helix, which is shorter than in the wild type protein. These two features allow us to propose a detailed structural interpretation for the stabilization of the native and especially the intermediate states induced by a single crucial mutation. These results show how protein engineering, x-ray crystallography and state-of-the-art kinetics concur to unveil a folding intermediate and the structural determinants of its stability.


    Related Citations: 
    • Selected mutations in a mesophilic cytochrome c confer the stability of a thermophilic counterpart.
      Hasegawa, J.,Uchiyama, S.,Tanimoto, Y.,Mizutani, M.,Kobayashi, Y.,Sambongi, Y.,Igarashi, Y.
      (2000) J.Biol.Chem. 275: 37824
    • Structure of cytochrome c551 from Pseudomonas aeruginosa refined at 1.6 A resolution and comparison of the two redox forms.
      Matsuura, Y.,Takano, T.,Dickerson, R.E.
      (1982) J.Mol.Biol. 156: 389
    • An obligatory intermediate in the folding pathway of cytochrome c552 from Hydrogenobacter thermophilus.
      Travaglini-Allocatelli, C.,Gianni, S.,Dubey, V.K.,Borgia, A.,Di Matteo, A.,Bonivento, D.,Bren, K.L.,Brunori, M.
      (2005) J.Biol.Chem. 280: 25729


    Organizational Affiliation

    Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche, Università di Roma "La Sapienza," P.le A. Moro 5, 00185 Rome, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-551
A, C
82Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 1 
Gene Names: nirM
Find proteins for P00099 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  P00099
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download SDF File 
Download CCD File 
A, C
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A, C
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.175 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 66.766α = 90.00
b = 66.766β = 90.00
c = 62.462γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance