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 
  • R-Value Observed: 0.224 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 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: https://doi.org/10.1042/BST20160138
  • Primary Citation of Related Structures:  
    5WEH

  • PubMed Abstract: 

    Given the central role of cytochrome c oxidase (C c O) 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 C c O. The redox-induced structural changes are seen in both the two-subunit and a new four-subunit crystal structure of bacterial C c O 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 C c O.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1A,
B [auth G]
566Cereibacter sphaeroidesMutation(s): 0 
Gene Names: ctaD
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P33517 (Cereibacter sphaeroides)
Explore P33517 
Go to UniProtKB:  P33517
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33517
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2C [auth B],
F [auth H]
262Cereibacter sphaeroidesMutation(s): 0 
Gene Names: ctaCcoxIIctaB
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q03736 (Cereibacter sphaeroides)
Explore Q03736 
Go to UniProtKB:  Q03736
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03736
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3)D [auth C],
G [auth I]
266Cereibacter sphaeroidesMutation(s): 0 
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P84153 (Cereibacter sphaeroides)
Explore P84153 
Go to UniProtKB:  P84153
Entity Groups  
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UniProt GroupP84153
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Aa3-type cytochrome c oxidase subunit IVE [auth D],
H [auth J]
50Cereibacter sphaeroidesMutation(s): 0 
Gene Names: coxIV
Membrane Entity: Yes 
UniProt
Find proteins for Q8KRK5 (Cereibacter sphaeroides)
Explore Q8KRK5 
Go to UniProtKB:  Q8KRK5
Entity Groups  
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UniProt GroupQ8KRK5
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
Q [auth G],
R [auth G]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
3PE
Query on 3PE

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AA [auth C]
BA [auth C]
DA [auth D]
GA [auth I]
HA [auth I]
AA [auth C],
BA [auth C],
DA [auth D],
GA [auth I],
HA [auth I],
IA [auth I],
JA [auth J],
N [auth A],
O [auth A],
V [auth G],
W [auth G]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
LMU
Query on LMU

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CA [auth C],
P [auth G],
X [auth G]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
CU1
Query on CU1

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EA [auth H]
FA [auth H]
K [auth A]
S [auth G]
Y [auth B]
EA [auth H],
FA [auth H],
K [auth A],
S [auth G],
Y [auth B],
Z [auth B]
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
CA
Query on CA

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M [auth A],
U [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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L [auth A],
T [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 339.221α = 90
b = 339.221β = 90
c = 89.199γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP01GM57323

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Refinement description
  • Version 1.2: 2017-10-25
    Changes: Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2021-06-30
    Changes: Advisory, Derived calculations
  • Version 2.0: 2021-07-07
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 2.2: 2024-10-23
    Changes: Data collection, Structure summary