3S8G

1.8 A structure of ba3 cytochrome c oxidase mutant (A120F) from Thermus thermophilus in lipid environment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High resolution structure of the ba3 cytochrome c oxidase from Thermus thermophilus in a lipidic environment.

Tiefenbrunn, T.Liu, W.Chen, Y.Katritch, V.Stout, C.D.Fee, J.A.Cherezov, V.

(2011) Plos One 6: e22348-e22348

  • DOI: 10.1371/journal.pone.0022348
  • Primary Citation of Related Structures:  3S8F

  • PubMed Abstract: 
  • The fundamental chemistry underpinning aerobic life on Earth involves reduction of dioxygen to water with concomitant proton translocation. This process is catalyzed by members of the heme-copper oxidase (HCO) superfamily. Despite the availability of ...

    The fundamental chemistry underpinning aerobic life on Earth involves reduction of dioxygen to water with concomitant proton translocation. This process is catalyzed by members of the heme-copper oxidase (HCO) superfamily. Despite the availability of crystal structures for all types of HCO, the mode of action for this enzyme is not understood at the atomic level, namely how vectorial H(+) and e(-) transport are coupled. Toward addressing this problem, we report wild type and A120F mutant structures of the ba(3)-type cytochrome c oxidase from Thermus thermophilus at 1.8 Å resolution. The enzyme has been crystallized from the lipidic cubic phase, which mimics the biological membrane environment. The structures reveal 20 ordered lipid molecules that occupy binding sites on the protein surface or mediate crystal packing interfaces. The interior of the protein encloses 53 water molecules, including 3 trapped in the designated K-path of proton transfer and 8 in a cluster seen also in A-type enzymes that likely functions in egress of product water and proton translocation. The hydrophobic O(2)-uptake channel, connecting the active site to the lipid bilayer, contains a single water molecule nearest the Cu(B) atom but otherwise exhibits no residual electron density. The active site contains strong electron density for a pair of bonded atoms bridging the heme Fe(a3) and Cu(B) atoms that is best modeled as peroxide. The structure of ba(3)-oxidase reveals new information about the positioning of the enzyme within the membrane and the nature of its interactions with lipid molecules. The atomic resolution details provide insight into the mechanisms of electron transfer, oxygen diffusion into the active site, reduction of oxygen to water, and pumping of protons across the membrane. The development of a robust system for production of ba(3)-oxidase crystals diffracting to high resolution, together with an established expression system for generating mutants, opens the door for systematic structure-function studies.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 1
A
569Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: cbaA
EC: 1.9.3.1
Find proteins for Q5SJ79 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ79
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 2
B
168Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: cbaB (ctaC)
EC: 1.9.3.1
Find proteins for Q5SJ80 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ80
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide 2A
C
34Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: cbaD
EC: 1.9.3.1
Find proteins for P82543 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P82543
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HAS
Query on HAS

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A
HEME-AS
C54 H64 Fe N4 O6
PDYODZVCODUKFH-QIHJKJTBDH
 Ligand Interaction
OLC
Query on OLC

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A, B, C
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
CUA
Query on CUA

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Download CCD File 
B
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
PER
Query on PER

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A
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CU
Query on CU

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Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 144.963α = 90.00
b = 98.636β = 128.07
c = 95.060γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2012-03-21
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description