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Structure of M2 pyruvate kinase in complex with phenylalanine
Biology and Chemistry Report
4FXF
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE
    Text TIM Barrel, TRANSFERASE, ATP binding

    Polymeric Molecules

    Chain A,B,C,D
    Description Pyruvate kinase isozymes M1/M2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 60164.7 
    Source Method genetically manipulated  
    Entity Name Cytosolic thyroid hormone-binding protein, CTHBP, Opa-interacting protein 3, OIP-3, Pyruvate kinase 2/3, Pyruvate kinase muscle isozyme, Thyroid hormone-binding protein 1, THBP1, Tumor M2-PK, p58 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ATP  ADENOSINE-5'-TRIPHOSPHATE  C10 H16 N5 O13 P3   507.18  View 
    FBP  BETA-FRUCTOSE-1,6-DIPHOSPHATE  C6 H14 O12 P2   340.12  View 
    POTASSIUM ION  K   39.10  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    OXL  OXALATE ION  C2 O4   88.02  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D KPYM_HUMAN P14618     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B C D  2.7.1.40      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D
    GO ID   Ontology GO Term Definition
    1666   Response to Hypoxia  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Stimulus Indicating Lowered Oxygen Tension. Hypoxia Defined As a Decline in O2 Levels Below Normoxic Levels of 20.8 20.95% Results in Metabolic Adaptation At Both the Cellular and Organismal Level. 
    1889   Liver Development  The Process Whose Specific Outcome Is the Progression of the Liver Over Time From Its Formation to the Mature Structure. the Liver Is an Exocrine Gland Which Secretes Bile and Functions in Metabolism of Protein and Carbohydrate and Fat Synthesizes Substances Involved in the Clotting of the Blood Synthesizes Vitamin a Detoxifies Poisonous Substances Stores Glycogen and Breaks Down Worn Out Erythrocytes. 
    5975   Carbohydrate Metabolic Process  The Chemical Reactions and Pathways Involving Carbohydrates Any of a Group of Organic Compounds Based of the General Formula Cx(h2o)y. Includes the Formation of Carbohydrate Derivatives by the Addition of a Carbohydrate Residue to Another Molecule. 
    6006   Glucose Metabolic Process  The Chemical Reactions and Pathways Involving Glucose the Aldohexose Gluco Hexose. D Glucose Is Dextrorotatory and Is Sometimes Known As Dextrose; It Is an Important Source of Energy For Living Organisms and Is Found Free As Well As Combined in Homo and Hetero Oligosaccharides and Polysaccharides. 
    6096   Glycolytic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of a Carbohydrate Into Pyruvate with the Concomitant Production of a Small Amount of ATP and the Reduction of Nad(p) to Nad(p)h. Glycolysis Begins with the Metabolism of a Carbohydrate to Generate Products That Can Enter the Pathway and Ends with the Production of Pyruvate. Pyruvate May Be Converted to Acetyl Coenzyme a Ethanol Lactate or Other Small Molecules. 
    6754   ATP Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    7584   Response to Nutrient  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Nutrient Stimulus. 
    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. 
    9629   Response to Gravity  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Gravitational Stimulus. 
    10033   Response to Organic Substance  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of an Organic Substance Stimulus. 
    12501   Programmed Cell Death  A Process Which Begins When a Cell Receives an Internal or External Signal and Activates a Series of Biochemical Events (signaling Pathway). the Process Ends with the Death of the Cell. 
    14870   Response to Muscle Inactivity  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Muscle Inactivity Stimulus. 
    16310   Phosphorylation  The Process of Introducing a Phosphate Group Into a Molecule Usually with the Formation of a Phosphoric Ester a Phosphoric Anhydride or a Phosphoric Amide. 
    31100   Organ Regeneration  The Regrowth of a Lost or Destroyed Organ. 
    32868   Response to Insulin  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of an Insulin Stimulus. Insulin Is a Polypeptide Hormone Produced by the Islets of Langerhans of the Pancreas in Mammals and by the Homologous Organs of Other Organisms. 
    42866   Pyruvate Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Pyruvate 2 Oxopropanoate. 
    43403   Skeletal Muscle Tissue Regeneration  The Regrowth of Skeletal Muscle Tissue to Repair Injured or Damaged Muscle Fibers in the Postnatal Stage. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    61621   Canonical Glycolysis  The Glycolytic Process That Begins with the Conversion of Glucose to Glucose 6 Phosphate by Glucokinase Activity. Glycolytic Processes Are the Chemical Reactions and Pathways Resulting in the Breakdown of a Carbohydrate Into Pyruvate with the Concomitant Production of a Small Amount of Atp. 
    5634   Nucleus  A Membrane Bounded Organelle of Eukaryotic Cells in Which Chromosomes Are Housed and Replicated. in Most Cells the Nucleus Contains All of the Cell's Chromosomes Except the Organellar Chromosomes and Is the Site of RNA Synthesis and Processing. in Some Species or in Specialized Cell Types RNA Metabolism or DNA Replication May Be Absent. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5739   Mitochondrion  A Semiautonomous Self Replicating Organelle That Occurs in Varying Numbers Shapes and Sizes in the Cytoplasm of Virtually All Eukaryotic Cells. It Is Notably the Site of Tissue Respiration. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    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. 
    5929   Cilium  A Specialized Eukaryotic Organelle That Consists of a Filiform Extrusion of the Cell Surface and of Some Cytoplasmic Parts. Each Cilium Is Largely Bounded by an Extrusion of the Cytoplasmic (plasma) Membrane and Contains a Regular Longitudinal Array of Microtubules Anchored to a Basal Body. 
    31012   Extracellular Matrix  A Structure Lying External to One or More Cells Which Provides Structural Support For Cells or Tissues; May Be Completely External to the Cell (as in Animals and Bacteria) or Be Part of the Cell (as in Plants). 
    31982   Vesicle  Any Small Fluid Filled Spherical Organelle Enclosed by Membrane or Protein. 
    43209   Myelin Sheath  An Electrically Insulating Fatty Layer That Surrounds the Axons of Many Neurons. It Is an Outgrowth of Glial Cells: Schwann Cells Supply the Myelin For Peripheral Neurons While Oligodendrocytes Supply It to Those of the Central Nervous System. 
    70062   Extracellular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. Extracellular Exosomes Also Simply Called Exosomes Have a Diameter of About 40 100 Nm. 
    1903561   Extracellular Vesicle  Any Vesicle That Is Part of the Extracellular Region. 
    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. 
    4743   Pyruvate Kinase Activity  Catalysis of the Reaction: ATP + Pyruvate = Adp + Phosphoenolpyruvate. 
    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). 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    16301   Kinase Activity  Catalysis of the Transfer of a Phosphate Group Usually From ATP to a Substrate Molecule. 
    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. 
    23026   Mhc Class Ii Protein Complex Binding  Interacting Selectively and Non Covalently with the Class Ii Major Histocompatibility Complex. 
    30955   Potassium Ion Binding  Interacting Selectively and Non Covalently with Potassium (k+) Ions. 
    43531   Adp Binding  Interacting Selectively and Non Covalently with Adp Adenosine 5' Diphosphate. 
    44822   Poly(a) RNA Binding  Interacting Non Covalently with a Poly(a) RNA a RNA Molecule Which Has a Tail of Adenine Bases. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C,D
    Common Name Human
    Scientific Name Homo sapiens  
    Details Codon_optimised
    Gene oip3, pk2, pk3, pkm, pkm2, pyruvate kinase m2
    Host Scientific Name Escherichia coli  
    Host Strain Bl21 De3
    Host Vector Type Pet
    Host Plasmid Name pET28a_M2


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    15 15q22 5315     pyruvate kinase, muscle PKM