4GP5

Structure of Recombinant Cytochrome ba3 Oxidase mutant Y133W from Thermus thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Ligand Access to the Active Site in Thermus thermophilusba(3) and Bovine Heart aa(3) Cytochrome Oxidases.

McDonald, W.Funatogawa, C.Li, Y.Szundi, I.Chen, Y.Fee, J.A.Stout, C.D.Einarsdottir, O.

(2013) Biochemistry 52: 640-652

  • DOI: 10.1021/bi301358a
  • Primary Citation of Related Structures:  4GP4, 4GP8

  • PubMed Abstract: 
  • Knowledge of the structure and dynamics of the ligand channel(s) in heme-copper oxidases is critical for understanding how the protein environment modulates the functions of these enzymes. Using photolabile NO and O(2) carriers, we recently found tha ...

    Knowledge of the structure and dynamics of the ligand channel(s) in heme-copper oxidases is critical for understanding how the protein environment modulates the functions of these enzymes. Using photolabile NO and O(2) carriers, we recently found that NO and O(2) binding in Thermus thermophilus (Tt) ba(3) is ~10 times faster than in the bovine enzyme, indicating that inherent structural differences affect ligand access in these enzymes. Using X-ray crystallography, time-resolved optical absorption measurements, and theoretical calculations, we investigated ligand access in wild-type Tt ba(3) and the mutants, Y133W, T231F, and Y133W/T231F, in which tyrosine and threonine in the O(2) channel of Tt ba(3) are replaced by the corresponding bulkier tryptophan and phenylalanine, respectively, present in the aa(3) enzymes. NO binding in Y133W and Y133W/T231F was found to be 5 times slower than in wild-type ba(3) and the T231F mutant. The results show that the Tt ba(3) Y133W mutation and the bovine W126 residue physically impede NO access to the binuclear center. In the bovine enzyme, there is a hydrophobic "way station", which may further slow ligand access to the active site. Classical simulations of diffusion of Xe to the active sites in ba(3) and bovine aa(3) show conformational freedom of the bovine F238 and the F231 side chain of the Tt ba(3) Y133W/T231F mutant, with both residues rotating out of the ligand channel, resulting in no effect on ligand access in either enzyme.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 1
A
568Thermus 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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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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A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 144.090α = 90.00
b = 97.960β = 127.99
c = 94.650γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALAdata scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Database references
  • Version 1.2: 2013-02-13
    Type: Database references
  • Version 1.3: 2013-03-13
    Type: Non-polymer description