3OMI

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with D132A mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump.

Liu, J.Qin, L.Ferguson-Miller, S.

(2011) Proc.Natl.Acad.Sci.USA 108: 1284-1289

  • DOI: 10.1073/pnas.1012846108
  • Primary Citation of Related Structures:  3OM3, 3OMA, 3OMN

  • PubMed Abstract: 
  • Crystal structures in both oxidized and reduced forms are reported for two bacterial cytochrome c oxidase mutants that define the D and K proton paths, showing conformational change in response to reduction and the loss of strategic waters that can a ...

    Crystal structures in both oxidized and reduced forms are reported for two bacterial cytochrome c oxidase mutants that define the D and K proton paths, showing conformational change in response to reduction and the loss of strategic waters that can account for inhibition of proton transfer. In the oxidized state both mutants of the Rhodobacter sphaeroides enzyme, D132A and K362M, show overall structures similar to wild type, indicating no long-range effects of mutation. In the reduced state, the mutants show an altered conformation similar to that seen in reduced wild type, confirming this reproducible, reversible response to reduction. In the strongly inhibited D132A mutant, positions of residues and waters in the D pathway are unaffected except in the entry region close to the mutation, where a chloride ion replaces the missing carboxyl and a 2-Å shift in N207 results in loss of its associated water. In K362M, the methionine occupies the same position as the original lysine, but K362- and T359-associated waters in the wild-type structure are missing, likely accounting for the severe inhibition. Spectra of oxidized frozen crystals taken during X-ray radiation show metal center reduction, but indicate development of a strained configuration that only relaxes to a native form upon annealing. Resistance of the frozen crystal to structural change clarifies why the oxidized conformation is observable and supports the conclusion that the reduced conformation has functional significance. A mechanism is described that explains the conformational change and the incomplete response of the D-path mutant.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase, aa3 type, subunit I
A, C
535Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)Gene Names: coxI
EC: 1.9.3.1
Find proteins for Q3J5A7 (Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158))
Go to UniProtKB:  Q3J5A7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 2
B, D
256Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)Gene Names: coxII
EC: 1.9.3.1
Find proteins for Q3J5G0 (Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158))
Go to UniProtKB:  Q3J5G0
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

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A, C
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
DMU
Query on DMU

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A, B, C, D
DECYL-BETA-D-MALTOPYRANOSIDE
DECYLMALTOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
CL
Query on CL

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A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CU1
Query on CU1

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B, D
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
HTH
Query on HTH

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B
(2S,3R)-heptane-1,2,3-triol
heptane-1,2,3-triol
C7 H16 O3
HXYCHJFUBNTKQR-RQJHMYQMSA-N
 Ligand Interaction
CA
Query on CA

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A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
OH
Query on OH

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A, C
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
CU
Query on CU

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A, B, C, D
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
TRD
Query on TRD

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A, B, C, D
TRIDECANE
LIPID FRAGMENT
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

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B, D
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 125.064α = 90.00
b = 131.519β = 90.00
c = 175.674γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MD2data collection
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-05-02
    Type: Structure summary
  • Version 1.3: 2014-11-19
    Type: Non-polymer description
  • Version 1.4: 2017-11-08
    Type: Refinement description