1CYX

QUINOL OXIDASE (PERIPLASMIC FRAGMENT OF SUBUNIT II WITH ENGINEERED CU-A BINDING SITE)(CYOA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the membrane-exposed domain from a respiratory quinol oxidase complex with an engineered dinuclear copper center.

Wilmanns, M.Lappalainen, P.Kelly, M.Sauer-Eriksson, E.Saraste, M.

(1995) Proc.Natl.Acad.Sci.USA 92: 11955-11959

  • Primary Citation of Related Structures:  1CYW

  • PubMed Abstract: 
  • Cytochrome oxidase is a membrane protein complex that catalyzes reduction of molecular oxygen to water and utilizes the free energy of this reaction to generate a transmembrane proton gradient during respiration. The electron entry site in subunit II ...

    Cytochrome oxidase is a membrane protein complex that catalyzes reduction of molecular oxygen to water and utilizes the free energy of this reaction to generate a transmembrane proton gradient during respiration. The electron entry site in subunit II is a mixed-valence dinuclear copper center in enzymes that oxidize cytochrome c. This center has been lost during the evolution of the quinoloxidizing branch of cytochrome oxidases but can be restored by engineering. Herein we describe the crystal structures of the periplasmic fragment from the wild-type subunit II (CyoA) of Escherichia coli quinol oxidase at 2.5-A resolution and of the mutant with the engineered dinuclear copper center (purple CyoA) at 2.3-A resolution. CyoA is folded as an 11-stranded mostly antiparallel beta-sandwich followed by three alpha-helices. The dinuclear copper center is located at the loops between strands beta 5-beta 6 and beta 9-beta 10. The two coppers are at a 2.5-A distance and symmetrically coordinated to the main ligands that are two bridging cysteines and two terminal histidines. The residues that are distinct in cytochrome c and quinol oxidases are around the dinuclear copper center. Structural comparison suggests a common ancestry for subunit II of cytochrome oxidase and blue copper-binding proteins.


    Related Citations: 
    • Restoration of a Lost Metal-Binding Site: Construction of Two Different Copper Sites Into a Subunit of the E. Coli Cytochrome O Quinol Oxidase Complex
      Van Der Oost, J.,Lappalainen, P.,Musacchio, A.,Warne, A.,Lemieux, L.,Rumbley, J.,Gennis, R.B.,Aasa, R.,Pascher, T.,Malmstrom, B.M.,Saraste, M.
      (1992) Embo J. 11: 3209
    • Crystallization and Preliminary X-Ray Analysis of the Periplasmic Fragment of Cyoa-A Subunit of the Escherichia Coli Cytochrome O Complex
      Van Der Oost, J.,Musacchio, A.,Pauptit, R.A.,Ceska, T.A.,Wierenga, R.K.,Saraste, M.
      (1993) J.Mol.Biol. 229: 794
    • Two Cysteines, Two Histidines and One Methionine are Ligands of a Binuclear Purple Copper Center
      Kelly, M.,Lappalainen, P.,Talbo, G.,Haltia, T.,Van Der Oost, J.,Saraste, M.
      (1993) J.Biol.Chem. 268: 16781


    Organizational Affiliation

    European Molecular Biology Laboratory, Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYOA
A
205Escherichia coli (strain K12)Gene Names: cyoA
Find proteins for P0ABJ1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABJ1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CUA
Query on CUA

Download SDF File 
Download CCD File 
A
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.000α = 90.00
b = 98.200β = 90.00
c = 39.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
XDSdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance