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Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Keywords lyase
    Text Pyrococcus horikoshii, pdxS, pyridoxal biosynthesis lyase, pyridoxal 5 -phosphate (PLP), lyase

    Polymeric Molecules

    Chain A,B,C,D,E,F
    Description Pyridoxal biosynthesis lyase pdxS 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 37065.6 
    Source Method genetically manipulated  

  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D,E,F PDXS_PYRHO O59080     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B C D E F  4      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D,E,F
    GO ID   Ontology GO Term Definition
    8152   Metabolic Process  The Chemical Reactions and Pathways Including Anabolism and Catabolism by Which Living Organisms Transform Chemical Substances. Metabolic Processes Typically Transform Small Molecules But Also Include Macromolecular Processes Such As DNA Repair and Replication and Protein Synthesis and Degradation. 
    9228   Thiamine Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Thiamine (vitamin B1) a Water Soluble Vitamin Present in Fresh Vegetables and Meats Especially Liver. 
    42819   Vitamin B6 Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Any of the Vitamin B6 Compounds; Pyridoxal Pyridoxamine and Pyridoxine and the Active Form Pyridoxal Phosphate. 
    42823   Pyridoxal Phosphate Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Pyridoxal Phosphate Pyridoxal Phosphorylated At the Hydroxymethyl Group of C 5 the Active Form of Vitamin B6. 
    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. 
    16829   Lyase Activity  Catalysis of the Cleavage of C C C O C N and Other Bonds by Other Means Than by Hydrolysis or Oxidation or Conversely Adding a Group to a Double Bond. They Differ From Other Enzymes in That Two Substrates Are Involved in One Reaction Direction But Only One in the Other Direction. When Acting On the Single Substrate a Molecule Is Eliminated and This Generates Either a New Double Bond or a New Ring. 
    36355   2 Iminoacetate Synthase Activity  Catalysis of the Reaction: L Tyrosine + S Adenosyl L Methionine + Reduced Acceptor = 2 Iminoacetate + 4 Methylphenol + 5' Deoxyadenosine + L Methionine + Acceptor + 2 H+. 
    36381   Pyridoxal 5' Phosphate Synthase (glutamine Hydrolysing) Activity  Catalysis of the Reaction: D Ribose 5 Phosphate + D Glyceraldehyde 3 Phosphate + L Glutamine = Pyridoxal 5' Phosphate + L Glutamate + 3 H2o + Phosphate. the Reaction Occurs in Two Steps: L Glutamine + H2o = L Glutamate + Nh3 and Subsequently D Ribose 5 Phosphate + D Glyceraldehyde 3 Phosphate + Nh3 = Pyridoxal 5' Phosphate + 4 H2o + Phosphate. 

  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C,D,E,F
    Scientific Name Pyrococcus horikoshii  
    Strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
    Gene pdxs, ph1355
    Host Scientific Name Escherichia coli  
    Host Vector Type Plasmid
    Host Plasmid Name pET-21a(+)

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    - - 1443680     pyridoxal biosynthesis protein PH_RS06425