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Structure of the ADPxAlF3-Stabilized Transition State of the Nitrogenase-like Dark-Operative Protochlorophyllide Oxidoreductase Complex from Prochlorococcus marinus with Its Substrate Protochlorophyllide a
Biology and Chemistry Report
2YNM
  •   Structure Details   Hide

    Structure Keywords

    Keywords OXIDOREDUCTASE
    Text IRON-SULFUR CLUSTER, OXIDOREDUCTASE, METALLOENZYME, ELECTRON TRANSFER, CHLOROPHYLL SYNTHESIS, ATPASE, DYNAMIC SWITCH

    Polymeric Molecules

    Chain A,B
    Description LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE IRON-SULFUR ATP-BINDING PROTEIN 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 32845.7 
    Source Method genetically manipulated  
    Entity Name DPOR SUBUNIT L, LI-POR SUBUNIT L 
    Chain C
    Description LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 47040.8 
    Source Method genetically manipulated  
    Entity Name DPOR SUBUNIT N, LI-POR SUBUNIT N 
    Chain D
    Description LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 58799.1 
    Source Method genetically manipulated  
    Entity Name DPOR SUBUNIT B, LI-POR SUBUNIT B 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    1PE  PENTAETHYLENE GLYCOL  C10 H22 O6   238.28  View 
    ADP  ADENOSINE-5'-DIPHOSPHATE  C10 H15 N5 O10 P2   427.20  View 
    AF3  ALUMINUM FLUORIDE  Al F3   83.98  View 
    EPE  4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID  C8 H18 N2 O4 S   238.31  View 
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    POTASSIUM ION  K   39.10  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    PMR  Protochlorophyllide  C35 H32 Mg N4 O5   612.96  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 CHLL_PROMA Q7VD39     
    C CHLN_PROMA Q7VD37     
    D CHLB_PROMA Q7VD38     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  1.3.7.7      
    1.3.7.7      
    1.3.7.7      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    15979   Photosynthesis  The Synthesis by Organisms of Organic Chemical Compounds Especially Carbohydrates From Carbon Dioxide (co2) Using Energy Obtained From Light Rather Than From the Oxidation of Chemical Compounds. 
    15995   Chlorophyll Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Chlorophyll Any Compound of Magnesium Complexed in a Porphyrin (tetrapyrrole) Ring and Which Functions As a Photosynthetic Pigment From Less Complex Precursors. 
    19685   Photosynthesis Dark Reaction  A Complex Cycle of Enzyme Mediated Reactions Which Catalyzes the Reduction of Carbon Dioxide to Sugar. As Well As Carbon Dioxide the Cycle Requires Reducing Power in the Form of Reduced Nicotinamide Adenine Dinucleotide Phosphate (nadp) and Chemical Energy in the Form of Adenosine Triphosphate (atp). the Reduced Nadp (nadph) and ATP Are Produced by the 'light' Reactions. 
    36068   Light Independent Chlorophyll Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Chlorophyll Any Compound of Magnesium Complexed in a Porphyrin (tetrapyrrole) Ring and Which Functions As a Photosynthetic Pigment From Less Complex Precursors Which Occur in the Absence of Light. 
    46148   Pigment Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of a Pigment Any General or Particular Coloring Matter in Living Organisms E.g. Melanin. 
    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. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    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. 
    16636   Oxidoreductase Activity Acting On the Ch Ch Group of Donors Iron Sulfur Protein As Acceptor  Catalysis of an Oxidation Reduction (redox) Reaction in Which a Ch Ch Group Acts As a Hydrogen or Electron Donor and Reduces an Iron Sulfur Protein. 
    16730   Oxidoreductase Activity Acting On Iron Sulfur Proteins As Donors  Catalysis of an Oxidation Reduction (redox) Reaction in Which an Iron Sulfur Protein Acts As a Hydrogen or Electron Donor and Reduces a Hydrogen or Electron Acceptor. 
    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. 
    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. 
    Chain C
    GO ID   Ontology GO Term Definition
    15979   Photosynthesis  The Synthesis by Organisms of Organic Chemical Compounds Especially Carbohydrates From Carbon Dioxide (co2) Using Energy Obtained From Light Rather Than From the Oxidation of Chemical Compounds. 
    15995   Chlorophyll Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Chlorophyll Any Compound of Magnesium Complexed in a Porphyrin (tetrapyrrole) Ring and Which Functions As a Photosynthetic Pigment From Less Complex Precursors. 
    19685   Photosynthesis Dark Reaction  A Complex Cycle of Enzyme Mediated Reactions Which Catalyzes the Reduction of Carbon Dioxide to Sugar. As Well As Carbon Dioxide the Cycle Requires Reducing Power in the Form of Reduced Nicotinamide Adenine Dinucleotide Phosphate (nadp) and Chemical Energy in the Form of Adenosine Triphosphate (atp). the Reduced Nadp (nadph) and ATP Are Produced by the 'light' Reactions. 
    36068   Light Independent Chlorophyll Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Chlorophyll Any Compound of Magnesium Complexed in a Porphyrin (tetrapyrrole) Ring and Which Functions As a Photosynthetic Pigment From Less Complex Precursors Which Occur in the Absence of Light. 
    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. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    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. 
    16636   Oxidoreductase Activity Acting On the Ch Ch Group of Donors Iron Sulfur Protein As Acceptor  Catalysis of an Oxidation Reduction (redox) Reaction in Which a Ch Ch Group Acts As a Hydrogen or Electron Donor and Reduces an Iron Sulfur Protein. 
    16730   Oxidoreductase Activity Acting On Iron Sulfur Proteins As Donors  Catalysis of an Oxidation Reduction (redox) Reaction in Which an Iron Sulfur Protein Acts As a Hydrogen or Electron Donor and Reduces a Hydrogen or Electron Acceptor. 
    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. 
    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. 
    Chain D
    GO ID   Ontology GO Term Definition
    15979   Photosynthesis  The Synthesis by Organisms of Organic Chemical Compounds Especially Carbohydrates From Carbon Dioxide (co2) Using Energy Obtained From Light Rather Than From the Oxidation of Chemical Compounds. 
    15995   Chlorophyll Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Chlorophyll Any Compound of Magnesium Complexed in a Porphyrin (tetrapyrrole) Ring and Which Functions As a Photosynthetic Pigment From Less Complex Precursors. 
    19685   Photosynthesis Dark Reaction  A Complex Cycle of Enzyme Mediated Reactions Which Catalyzes the Reduction of Carbon Dioxide to Sugar. As Well As Carbon Dioxide the Cycle Requires Reducing Power in the Form of Reduced Nicotinamide Adenine Dinucleotide Phosphate (nadp) and Chemical Energy in the Form of Adenosine Triphosphate (atp). the Reduced Nadp (nadph) and ATP Are Produced by the 'light' Reactions. 
    36068   Light Independent Chlorophyll Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Chlorophyll Any Compound of Magnesium Complexed in a Porphyrin (tetrapyrrole) Ring and Which Functions As a Photosynthetic Pigment From Less Complex Precursors Which Occur in the Absence of Light. 
    46148   Pigment Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of a Pigment Any General or Particular Coloring Matter in Living Organisms E.g. Melanin. 
    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. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    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. 
    16636   Oxidoreductase Activity Acting On the Ch Ch Group of Donors Iron Sulfur Protein As Acceptor  Catalysis of an Oxidation Reduction (redox) Reaction in Which a Ch Ch Group Acts As a Hydrogen or Electron Donor and Reduces an Iron Sulfur Protein. 
    16730   Oxidoreductase Activity Acting On Iron Sulfur Proteins As Donors  Catalysis of an Oxidation Reduction (redox) Reaction in Which an Iron Sulfur Protein Acts As a Hydrogen or Electron Donor and Reduces a Hydrogen or Electron Acceptor. 
    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. 
    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 D
    Scientific Name Prochlorococcus marinus  
    Host Scientific Name Escherichia coli  
    Host Variant Codon Plus Ril
    Host Strain Bl21(de3)
    Host Vector Pgex 6p 1
    Host Vector Type Plasmid


    Chain C
    Scientific Name Prochlorococcus marinus  
    Host Scientific Name Escherichia coli  
    Host Variant Codon Plus Ril
    Host Strain Bl21(de3)
    Host Vector Pgex 6p 1
    Host Vector Type Plasmid


    Chain A,B
    Scientific Name Prochlorococcus marinus  
    Host Scientific Name Escherichia coli  
    Host Variant Codon Plus Ril
    Host Strain Bl21(de3)
    Host Vector Pgex 6p 1
    Host Vector Type Plasmid


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    - - 1461926     ChlL CHLL    
    - - 1461928     ChlN CHLN    
    - - 1461927     ChlB CHLB