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Structure of Recombinant Cytochrome ba3 Oxidase mutant Y133W from Thermus thermophilus
Biology and Chemistry Report
4GP5
  •   Structure Details   Hide

    Structure Keywords

    Keywords OXIDOREDUCTASE
    Text OXIDOREDUCTASE, Proton Pump

    Polymeric Molecules

    Chain A
    Description Cytochrome c oxidase subunit 1 
    Mutation Y133W 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 63425.8 
    Source Method genetically manipulated  
    Entity Name Cytochrome c ba(3) subunit I, Cytochrome c oxidase polypeptide I, Cytochrome cba3 subunit 1 
    Chain B
    Description Cytochrome c oxidase subunit 2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 18581.5 
    Source Method genetically manipulated  
    Entity Name Cytochrome c ba(3) subunit II, Cytochrome c oxidase polypeptide II, Cytochrome cba3 subunit 2 
    Chain C
    Description Cytochrome c oxidase polypeptide 2A 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 3769.6 
    Source Method genetically manipulated  
    Entity Name Cytochrome c ba(3) subunit IIA, Cytochrome c oxidase polypeptide IIA, Cytochrome cba3 subunit 2A 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CU  COPPER (II) ION  Cu   63.55  View 
    CUA  DINUCLEAR COPPER ION  Cu2   127.09  View 
    HAS  HEME-AS  C54 H64 Fe N4 O6   920.95  View 
    HEM  PROTOPORPHYRIN IX CONTAINING FE  C34 H32 Fe N4 O4   616.49  View 
    OLC  (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate  C21 H40 O4   356.54  View 
    PER  PEROXIDE ION  O2   32.00  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A COX1_THET8 Q5SJ79     
    B COX2_THET8 Q5SJ80     
    C COXA_THET8 P82543     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    1.9.3.1      
    1.9.3.1      
    1.9.3.1      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6119   Oxidative Phosphorylation  The Phosphorylation of Adp to ATP That Accompanies the Oxidation of a Metabolite Through the Operation of the Respiratory Chain. Oxidation of Compounds Establishes a Proton Gradient Across the Membrane Providing the Energy For ATP Synthesis. 
    6811   Ion Transport  The Directed Movement of Charged Atoms or Small Charged Molecules Into Out of or Within a Cell or Between Cells by Means of Some Agent Such As a Transporter or Pore. 
    9060   Aerobic Respiration  The Enzymatic Release of Energy From Inorganic and Organic Compounds (especially Carbohydrates and Fats) Which Requires Oxygen As the Terminal Electron Acceptor. 
    15992   Proton Transport  The Directed Movement of Protons (hydrogen Ions) Into Out of or Within a Cell or Between Cells by Means of Some Agent Such As a Transporter or Pore. 
    55114   Oxidation Reduction Process  A Metabolic Process That Results in the Removal or Addition of One or More Electrons to or From a Substance with or Without the Concomitant Removal or Addition of a Proton or Protons. 
    1902600   Hydrogen Ion Transmembrane Transport  The Directed Movement of Hydrogen Ion (proton) Across a Membrane. 
    5886   Plasma Membrane  The Membrane Surrounding a Cell That Separates the Cell From Its External Environment. It Consists of a Phospholipid Bilayer and Associated Proteins. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    16021   Integral Component of Membrane  The Component of a Membrane Consisting of Gene Products and Protein Complexes That Have Some Part That Penetrates At Least One Leaflet of the Membrane Bilayer. This Component Includes Gene Products That Are Buried in the Bilayer with No Exposure Outside the Bilayer. 
    70469   Respiratory Chain  The Protein Complexes That Form the Electron Transport System (the Respiratory Chain) Associated with a Cell Membrane Usually the Plasma Membrane (in Prokaryotes) or the Inner Mitochondrial Membrane (on Eukaryotes). the Respiratory Chain Complexes Transfer Electrons From an Electron Donor to an Electron Acceptor and Are Associated with a Proton Pump to Create a Transmembrane Electrochemical Gradient. 
    4129   Cytochrome C Oxidase Activity  Catalysis of the Reaction: 4 Ferrocytochrome C + O2 + 4 H+ = 4 Ferricytochrome C + 2 H2o. 
    5506   Iron Ion Binding  Interacting Selectively and Non Covalently with Iron (fe) Ions. 
    9055   Electron Carrier Activity  Any Molecular Entity That Serves As an Electron Acceptor and Electron Donor in an Electron Transport Chain. an Electron Transport Chain Is a Process in Which a Series of Electron Carriers Operate Together to Transfer Electrons From Donors to Any of Several Different Terminal Electron Acceptors to Generate a Transmembrane Electrochemical Gradient. 
    16491   Oxidoreductase Activity  Catalysis of an Oxidation Reduction (redox) Reaction a Reversible Chemical Reaction in Which the Oxidation State of an Atom or Atoms Within a Molecule Is Altered. One Substrate Acts As a Hydrogen or Electron Donor and Becomes Oxidized While the Other Acts As Hydrogen or Electron Acceptor and Becomes Reduced. 
    20037   Heme Binding  Interacting Selectively and Non Covalently with Heme Any Compound of Iron Complexed in a Porphyrin (tetrapyrrole) Ring. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    Chain B
    GO ID   Ontology GO Term Definition
    22900   Electron Transport Chain  A Process in Which a Series of Electron Carriers Operate Together to Transfer Electrons From Donors to Any of Several Different Terminal Electron Acceptors to Generate a Transmembrane Electrochemical Gradient. 
    55114   Oxidation Reduction Process  A Metabolic Process That Results in the Removal or Addition of One or More Electrons to or From a Substance with or Without the Concomitant Removal or Addition of a Proton or Protons. 
    1902600   Hydrogen Ion Transmembrane Transport  The Directed Movement of Hydrogen Ion (proton) Across a Membrane. 
    5886   Plasma Membrane  The Membrane Surrounding a Cell That Separates the Cell From Its External Environment. It Consists of a Phospholipid Bilayer and Associated Proteins. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    16021   Integral Component of Membrane  The Component of a Membrane Consisting of Gene Products and Protein Complexes That Have Some Part That Penetrates At Least One Leaflet of the Membrane Bilayer. This Component Includes Gene Products That Are Buried in the Bilayer with No Exposure Outside the Bilayer. 
    70469   Respiratory Chain  The Protein Complexes That Form the Electron Transport System (the Respiratory Chain) Associated with a Cell Membrane Usually the Plasma Membrane (in Prokaryotes) or the Inner Mitochondrial Membrane (on Eukaryotes). the Respiratory Chain Complexes Transfer Electrons From an Electron Donor to an Electron Acceptor and Are Associated with a Proton Pump to Create a Transmembrane Electrochemical Gradient. 
    4129   Cytochrome C Oxidase Activity  Catalysis of the Reaction: 4 Ferrocytochrome C + O2 + 4 H+ = 4 Ferricytochrome C + 2 H2o. 
    5507   Copper Ion Binding  Interacting Selectively and Non Covalently with Copper (cu) Ions. 
    16491   Oxidoreductase Activity  Catalysis of an Oxidation Reduction (redox) Reaction a Reversible Chemical Reaction in Which the Oxidation State of an Atom or Atoms Within a Molecule Is Altered. One Substrate Acts As a Hydrogen or Electron Donor and Becomes Oxidized While the Other Acts As Hydrogen or Electron Acceptor and Becomes Reduced. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    Chain C
    GO ID   Ontology GO Term Definition
    6811   Ion Transport  The Directed Movement of Charged Atoms or Small Charged Molecules Into Out of or Within a Cell or Between Cells by Means of Some Agent Such As a Transporter or Pore. 
    15992   Proton Transport  The Directed Movement of Protons (hydrogen Ions) Into Out of or Within a Cell or Between Cells by Means of Some Agent Such As a Transporter or Pore. 
    55114   Oxidation Reduction Process  A Metabolic Process That Results in the Removal or Addition of One or More Electrons to or From a Substance with or Without the Concomitant Removal or Addition of a Proton or Protons. 
    1902600   Hydrogen Ion Transmembrane Transport  The Directed Movement of Hydrogen Ion (proton) Across a Membrane. 
    5886   Plasma Membrane  The Membrane Surrounding a Cell That Separates the Cell From Its External Environment. It Consists of a Phospholipid Bilayer and Associated Proteins. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    16021   Integral Component of Membrane  The Component of a Membrane Consisting of Gene Products and Protein Complexes That Have Some Part That Penetrates At Least One Leaflet of the Membrane Bilayer. This Component Includes Gene Products That Are Buried in the Bilayer with No Exposure Outside the Bilayer. 
    70469   Respiratory Chain  The Protein Complexes That Form the Electron Transport System (the Respiratory Chain) Associated with a Cell Membrane Usually the Plasma Membrane (in Prokaryotes) or the Inner Mitochondrial Membrane (on Eukaryotes). the Respiratory Chain Complexes Transfer Electrons From an Electron Donor to an Electron Acceptor and Are Associated with a Proton Pump to Create a Transmembrane Electrochemical Gradient. 
    4129   Cytochrome C Oxidase Activity  Catalysis of the Reaction: 4 Ferrocytochrome C + O2 + 4 H+ = 4 Ferricytochrome C + 2 H2o. 
    16491   Oxidoreductase Activity  Catalysis of an Oxidation Reduction (redox) Reaction a Reversible Chemical Reaction in Which the Oxidation State of an Atom or Atoms Within a Molecule Is Altered. One Substrate Acts As a Hydrogen or Electron Donor and Becomes Oxidized While the Other Acts As Hydrogen or Electron Acceptor and Becomes Reduced. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain C
    Scientific Name Thermus thermophilus  
    Strain HB8 / ATCC 27634 / DSM 579
    Gene cbad, ttha1133
    Host Scientific Name Thermus thermophilus  
    Host Strain Mt111
    Host Vector Type Plasmid
    Host Plasmid Name pmk18


    Chain B
    Scientific Name Thermus thermophilus  
    Strain HB8 / ATCC 27634 / DSM 579
    Gene cbab, ctac, ttha1134
    Host Scientific Name Thermus thermophilus  
    Host Strain Mt111
    Host Vector Type Plasmid
    Host Plasmid Name pmk18


    Chain A
    Scientific Name Thermus thermophilus  
    Strain HB8 / ATCC 27634 / DSM 579
    Gene cbaa, ttha1135
    Host Scientific Name Thermus thermophilus  
    Host Strain Mt111
    Host Vector Type Plasmid
    Host Plasmid Name pmk18


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    - - 3168993     ba3-type cytochrome C oxidase polypeptide I TTHA1135    
    - - 3169672     ba3-type cytochrome C oxidase polypeptide II TTHA1134    
    - - 3168186     ba3-type cytochrome C oxidase polypeptide IIA TTHA1133