2HL7

Crystal structure of the periplasmic domain of CcmH from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A strategic protein in cytochrome c maturation: three-dimensional structure of CcmH and binding to apocytochrome c

Di Matteo, A.Gianni, S.Schinina, M.E.Giorgi, A.Altieri, F.Calosci, N.Brunori, M.Travaglini-Allocatelli, C.

(2007) J.Biol.Chem. 282: 27012-27019

  • DOI: 10.1074/jbc.M702702200

  • PubMed Abstract: 
  • CcmH (cytochromes c maturation protein H) is an essential component of the assembly line necessary for the maturation of c-type cytochromes in the periplasm of Gram-negative bacteria. The protein is a membrane-anchored thiol-oxidoreductase that has b ...

    CcmH (cytochromes c maturation protein H) is an essential component of the assembly line necessary for the maturation of c-type cytochromes in the periplasm of Gram-negative bacteria. The protein is a membrane-anchored thiol-oxidoreductase that has been hypothesized to be involved in the recognition and reduction of apocytochrome c, a prerequisite for covalent heme attachment. Here, we present the 1.7A crystal structure of the soluble periplasmic domain of CcmH from the opportunistic pathogen Pseudomonas aeruginosa (Pa-CcmH*). The protein contains a three-helix bundle, i.e. a fold that is different from that of all other thiol-oxidoreductases reported so far. The catalytic Cys residues of the conserved LRCXXC motif (Cys(25) and Cys(28)), located in a long loop connecting the first two helices, form a disulfide bond in the oxidized enzyme. We have determined the pK(a) values of these 2 Cys residues of Pa-CcmH* (both >8) and propose a possible mechanistic role for a conserved Ser(36) and a water molecule in the active site. The interaction between Pa-CcmH* and Pa-apocyt c(551) (where cyt c(551) represents cytochrome c(551)) was characterized in vitro following the binding kinetics by stopped-flow using a Trp-containing fluorescent variant of Pa-CcmH* and a dansylated peptide, mimicking the apocytochrome c(551) heme binding motif. The kinetic results show that the protein has a moderate affinity to its apocyt substrate, consistent with the role of Pa-CcmH as an intermediate component of the assembly line for c-type cytochrome biogenesis.


    Related Citations: 
    • Characterization of the Escherichia coli CcmH protein reveals new insights into the redox pathway required for cytochrome c maturation
      Fabianek, R.A.,Hofer, T.,Thony-Meyer, L.
      (1999) Arch.Microbiol. 171: 92
    • AtCCMH, an essential component of the c-type cytochrome maturation pathway in Arabidopsis mitochondria, interacts with apocytochrome c
      Meyer, E.H.,Giege, P.,Gelhaye, E.,Rayapuram, N.,Ahuja, U.,Thony-Meyer, L.,Grienenberger, J.M.,Bonnard, G.
      (2005) Proc.Natl.Acad.Sci.USA 102: 16113


    Organizational Affiliation

    Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, La Sapienza, Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome C-type biogenesis protein CcmH
A
84Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: ccmH
Find proteins for Q9I3N0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9I3N0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.073α = 90.00
b = 45.414β = 90.00
c = 48.127γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-10
    Type: Initial release
  • Version 1.1: 2007-10-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance