An Information Portal to 110790 Biological Macromolecular Structures

Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with oxoglutarate
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE
    Text menaquinone, ThDP, Mg, vitamin K2, carboxylase, Magnesium, Manganese, Menaquinone biosynthesis, Metal-binding, Thiamine pyrophosphate, Transferase

    Polymeric Molecules

    Chain A,D
    Description 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase 
    Mutation P36L 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 61450.5 
    Source Method genetically manipulated  
    Entity Name SEPHCHC synthase, Menaquinone biosynthesis protein menD 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    AKG  2-OXOGLUTARIC ACID  C5 H6 O5   146.10  View 
    CL  CHLORIDE ION  Cl   35.45  View 
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    NA  SODIUM ION  Na   22.99  View 
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,D MEND_ECOLI P17109     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    A D        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,D
    GO ID   Ontology GO Term Definition
    9234   Menaquinone Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Any of the Menaquinones. Structurally Menaquinones Consist of a Methylated Naphthoquinone Ring Structure and Side Chains Composed of a Variable Number of Unsaturated Isoprenoid Residues. Menaquinones That Have Vitamin K Activity and Are Known As Vitamin K2. 
    287   Magnesium Ion Binding  Interacting Selectively and Non Covalently with Magnesium (mg) Ions. 
    3824   Catalytic Activity  Catalysis of a Biochemical Reaction At Physiological Temperatures. in Biologically Catalyzed Reactions the Reactants Are Known As Substrates and the Catalysts Are Naturally Occurring Macromolecular Substances Known As Enzymes. Enzymes Possess Specific Binding Sites For Substrates and Are Usually Composed Wholly or Largely of Protein But RNA That Has Catalytic Activity (ribozyme) Is Often Also Regarded As Enzymatic. 
    16740   Transferase Activity  Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 
    30145   Manganese Ion Binding  Interacting Selectively and Non Covalently with Manganese (mn) Ions. 
    30976   Thiamine Pyrophosphate Binding  Interacting Selectively and Non Covalently with Thiamine Pyrophosphate the Diphosphoric Ester of Thiamine. Acts As a Coenzyme of Several (de)carboxylases Transketolases and Alpha Oxoacid Dehydrogenases. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    70204   2 Succinyl 5 Enolpyruvyl 6 Hydroxy 3 Cyclohexene 1 Carboxylic Acid Synthase Activity  Catalysis of the Reaction: 2 Oxoglutarate + H(+) + Isochorismate = 5 Enolpyruvoyl 6 Hydroxy 2 Succinyl Cyclohex 3 Ene 1 Carboxylate + Co(2). 

  •   Gene Details   Hide

    Genetic Source

    Chain A,D
    Scientific Name Escherichia coli k-12  
    Gene b2264, jw5374, mend
    Host Scientific Name Escherichia coli  
    Host Strain Bl21 (de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET28a