5WEH

Cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Role of conformational change and K-path ligands in controlling cytochrome c oxidase activity.

Liu, J.Hiser, C.Ferguson-Miller, S.

(2017) Biochem. Soc. Trans. 45: 1087-1095

  • DOI: 10.1042/BST20160138

  • PubMed Abstract: 
  • Given the central role of cytochrome c oxidase (CcO) in health and disease, it is an increasingly important question as to how the activity and efficiency of this key enzyme are regulated to respond to a variety of metabolic states. The present paper ...

    Given the central role of cytochrome c oxidase (CcO) in health and disease, it is an increasingly important question as to how the activity and efficiency of this key enzyme are regulated to respond to a variety of metabolic states. The present paper summarizes evidence for two modes of regulation of activity: first, by redox-induced conformational changes involving the K-proton uptake path; and secondly, by ligand binding to a conserved site immediately adjacent to the entrance of the K-path that leads to the active site. Both these phenomena highlight the importance of the K-path in control of CcO. The redox-induced structural changes are seen in both the two-subunit and a new four-subunit crystal structure of bacterial CcO and suggest a gating mechanism to control access of protons to the active site. A conserved ligand-binding site, first discovered as a bile salt/steroid site in bacterial and mammalian oxidases, is observed to bind an array of ligands, including nucleotides, detergents, and other amphipathic molecules. Highly variable effects on activity, seen for these ligands and mutations at the K-path entrance, can be explained by differing abilities to inhibit or stimulate K-path proton uptake by preventing or allowing water organization. A new mutant form in which the K-path is blocked by substituting the conserved carboxyl with a tryptophan clarifies the singularity of the K-path entrance site. Further study in eukaryotic systems will determine the physiological significance and pharmacological potential of ligand binding and conformational change in CcO.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, MI 48824, U.S.A.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 1
A, G
566Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: ctaD
EC: 1.9.3.1
Find proteins for P33517 (Rhodobacter sphaeroides)
Go to UniProtKB:  P33517
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 2
B, H
262Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: ctaC (coxII, ctaB)
EC: 1.9.3.1
Find proteins for Q03736 (Rhodobacter sphaeroides)
Go to UniProtKB:  Q03736
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3)
C, I
266Rhodobacter sphaeroidesMutation(s): 0 
EC: 1.9.3.1
Find proteins for P84153 (Rhodobacter sphaeroides)
Go to UniProtKB:  P84153
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Aa3-type cytochrome c oxidase subunit IV
D, J
50Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: coxIV
Find proteins for Q8KRK5 (Rhodobacter sphaeroides)
Go to UniProtKB:  Q8KRK5
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

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Download CCD File 
A, G
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
PEH
Query on PEH

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Download CCD File 
A, C, D, G, I, J
DI-STEAROYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
CU1
Query on CU1

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Download CCD File 
A, B, G, H
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
LMU
Query on LMU

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Download CCD File 
C, G
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 339.221α = 90.00
b = 339.221β = 90.00
c = 89.199γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP01GM57323

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Refinement description
  • Version 1.2: 2017-10-25
    Type: Database references