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Structure of E. coli hydrogenase-1 in complex with cytochrome b
Biology and Chemistry Report
4GD3
  •   Structure Details   Hide

    Structure Keywords

    Keywords OXIDOREDUCTASE/ELECTRON TRANSPORT
    Text O2-tolerant H2:quinone oxidoreductase, membrane-bound, Ni-Fe-hydrogenase-cytochrome B complex, OXIDOREDUCTASE-ELECTRON TRANSPORT complex

    Polymeric Molecules

    Chain Q,R,S,T
    Description Hydrogenase-1 small chain 
    Mutation P287C 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 36821.0 
    Source Method genetically manipulated  
    Entity Name HYD1, Membrane-bound hydrogenase 1 small subunit, NiFe hydrogenase 
    Chain J,K,L,M
    Description Hydrogenase-1 large chain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 64752.0 
    Source Method genetically manipulated  
    Entity Name HYD1, Membrane-bound hydrogenase 1 large subunit, NiFe hydrogenase 
    Chain A,B
    Description Ni/Fe-hydrogenase 1 B-type cytochrome subunit 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 27626.5 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CL  CHLORIDE ION  Cl   35.45  View 
    F4S  FE4-S3 CLUSTER  Fe4 S3   319.58  View 
    FCO  CARBONMONOXIDE-(DICYANO) IRON  C3 Fe N2 O   135.89  View 
    HEM  PROTOPORPHYRIN IX CONTAINING FE  C34 H32 Fe N4 O4   616.49  View 
    LMT  DODECYL-BETA-D-MALTOSIDE  C24 H46 O11   510.62  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    NI  NICKEL (II) ION  Ni   58.69  View 
    SF4  IRON/SULFUR CLUSTER  Fe4 S4   351.64  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B CYBH_ECOLI P0AAM1     
    J,K,L,M MBHL_ECOLI P0ACD8     
    Q,R,S,T MBHS_ECOLI P19928     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    Q R S T  1.12.99.6      
    J K L M  1.12.99.6      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    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. 
    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. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    Chain J,K,L,M
    GO ID   Ontology GO Term Definition
    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. 
    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. 
    5515   Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    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 Q,R,S,T
    GO ID   Ontology GO Term Definition
    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. 
    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. 
    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. 
    51536   Iron Sulfur Cluster Binding  Interacting Selectively and Non Covalently with an Iron Sulfur Cluster a Combination of Iron and Sulfur Atoms. 
    51538   3 Iron 4 Sulfur Cluster Binding  Interacting Selectively and Non Covalently with a 3 Iron 4 Sulfur (3fe 4s) Cluster; This Cluster Consists of Three Iron Atoms with the Inorganic Sulfur Atoms Found Between the Irons and Acting As Bridging Ligands. It Is Essentially a 4fe 4s Cluster with One Iron Missing. 
    51539   4 Iron 4 Sulfur Cluster Binding  Interacting Selectively and Non Covalently with a 4 Iron 4 Sulfur (4fe 4s) Cluster; This Cluster Consists of Four Iron Atoms with the Inorganic Sulfur Atoms Found Between the Irons and Acting As Bridging Ligands. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Scientific Name Escherichia coli  
    Strain K12
    Gene b0974, hyac, jw0956
    Host Scientific Name Escherichia coli  
    Host Strain Fth004


    Chain J,K,L,M
    Scientific Name Escherichia coli  
    Strain K12
    Gene b0973, hyab, jw0955
    Host Scientific Name Escherichia coli  
    Host Strain Fth004


    Chain Q,R,S,T
    Scientific Name Escherichia coli  
    Strain K12
    Gene b0972, hyaa, jw0954
    Host Scientific Name Escherichia coli  
    Host Strain Fth004