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Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with phosphate
Biology and Chemistry Report
4GKA
  •   Structure Details   Hide

    Structure Keywords

    Keywords transferase
    Text purine nucleoside phosphorylase, nucleoside binding, purine base binding, purine-nucleoside phosphorylase activity, drug binding, transferase activity, transferring glycosyl groups, phosphate ion binding, intracellular, cytosol, transferase

    Polymeric Molecules

    Chain A,B,C,D,E,F
    Description Purine nucleoside phosphorylase 
    Fragment NONE 
    Mutation W16Y, W94Y, W178Y, H257W 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 36127.4 
    Source Method genetically manipulated  
    Entity Name PNP, Inosine phosphorylase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    PO4  PHOSPHATE ION  O4 P   94.97  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D,E,F PNPH_HUMAN B2R8S5     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B C D E F  2.4.2.1      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D,E,F
    GO ID   Ontology GO Term Definition
    6139   Nucleobase Containing Compound Metabolic Process  Any Cellular Metabolic Process Involving Nucleobases Nucleosides Nucleotides and Nucleic Acids. 
    6144   Purine Nucleobase Metabolic Process  The Chemical Reactions and Pathways Involving Purine Nucleobases One of the Two Classes of Nitrogen Containing Ring Compounds Found in DNA and RNA Which Include Adenine and Guanine. 
    6148   Inosine Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Inosine Hypoxanthine Riboside a Nucleoside Found Free But Not in Combination in Nucleic Acids Except in the Anticodons of Some Trnas. 
    6195   Purine Nucleotide Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of a Purine Nucleotide a Compound Consisting of Nucleoside (a Purine Base Linked to a Deoxyribose or Ribose Sugar) Esterified with a Phosphate Group At Either the 3' or 5' Hydroxyl Group of the Sugar. 
    6738   Nicotinamide Riboside Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Nicotinamide Riboside the Product of the Formation of a Glycosidic Bond Between Ribose and Nicotinamide. 
    6955   Immune Response  Any Immune System Process That Functions in the Calibrated Response of an Organism to a Potential Internal or Invasive Threat. 
    9116   Nucleoside Metabolic Process  The Chemical Reactions and Pathways Involving a Nucleoside a Nucleobase Linked to Either Beta D Ribofuranose (a Ribonucleoside) or 2 Deoxy Beta D Ribofuranose (a Deoxyribonucleoside) E.g. Adenosine Guanosine Inosine Cytidine Uridine and Deoxyadenosine Deoxyguanosine Deoxycytidine and Thymidine (= Deoxythymidine). 
    34356   NAD Biosynthesis Via Nicotinamide Riboside Salvage Pathway  The Chemical Reactions and Pathways Resulting in the Formation of Nicotinamide Adenine Dinucleotide (nad) From the Vitamin Precursor Nicotinamide Riboside. 
    34418   Urate Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Urate the Anion of Uric Acid 2 6 8 Trioxypurine. 
    42102   Positive Regulation of T Cell Proliferation  Any Process That Activates or Increases the Rate or Extent of T Cell Proliferation. 
    42493   Response to Drug  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 Drug Stimulus. a Drug Is a Substance Used in the Diagnosis Treatment or Prevention of a Disease. 
    43101   Purine Containing Compound Salvage  Any Process That Generates a Purine Containing Compound Any Nucleobase Nucleoside Nucleotide or Nucleic Acid That Contains a Purine Base From Derivatives of Them Without De Novo Synthesis. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    46638   Positive Regulation of Alpha Beta T Cell Differentiation  Any Process That Activates or Increases the Frequency Rate or Extent of Alpha Beta T Cell Differentiation. 
    55086   Nucleobase Containing Small Molecule Metabolic Process  The Cellular Chemical Reactions and Pathways Involving a Nucleobase Containing Small Molecule: a Nucleobase a Nucleoside or a Nucleotide. 
    70970   Interleukin 2 Secretion  The Regulated Release of Interleukin 2 From a Cell. 
    5622   Intracellular  The Living Contents of a Cell; the Matter Contained Within (but Not Including) the Plasma Membrane Usually Taken to Exclude Large Vacuoles and Masses of Secretory or Ingested Material. in Eukaryotes It Includes the Nucleus and Cytoplasm. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    5856   Cytoskeleton  Any of the Various Filamentous Elements That Form the Internal Framework of Cells and Typically Remain After Treatment of the Cells with Mild Detergent to Remove Membrane Constituents and Soluble Components of the Cytoplasm. the Term Embraces Intermediate Filaments Microfilaments Microtubules the Microtrabecular Lattice and Other Structures Characterized by a Polymeric Filamentous Nature and Long Range Order Within the Cell. the Various Elements of the Cytoskeleton Not Only Serve in the Maintenance of Cellular Shape But Also Have Roles in Other Cellular Functions Including Cellular Movement Cell Division Endocytosis and Movement of Organelles. 
    70062   Extracellular Vesicular 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. 
    1882   Nucleoside Binding  Interacting Selectively and Non Covalently with a Nucleoside a Compound Consisting of a Purine or Pyrimidine Nitrogenous Base Linked Either to Ribose or Deoxyribose. 
    2060   Purine Nucleobase Binding  Interacting Selectively and Non Covalently with a Purine Nucleobase an Organic Nitrogenous Base with a Purine Skeleton. 
    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. 
    4731   Purine Nucleoside Phosphorylase Activity  Catalysis of the Reaction: Purine Nucleoside + Phosphate = Purine + Alpha D Ribose 1 Phosphate. 
    8144   Drug Binding  Interacting Selectively and Non Covalently with a Drug Any Naturally Occurring or Synthetic Substance Other Than a Nutrient That When Administered or Applied to an Organism Affects the Structure or Functioning of the Organism; in Particular Any Such Substance Used in the Diagnosis Prevention or Treatment of Disease. 
    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. 
    16757   Transferase Activity Transferring Glycosyl Groups  Catalysis of the Transfer of a Glycosyl Group From One Compound (donor) to Another (acceptor). 
    16763   Transferase Activity Transferring Pentosyl Groups  Catalysis of the Transfer of a Pentosyl Group From One Compound (donor) to Another (acceptor). 
    42301   Phosphate Ion Binding  Interacting Selectively and Non Covalently with Phosphate. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C,D,E,F
    Common Name Human
    Scientific Name Homo sapiens  
    Gene np, pnp, x00737.1
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)plyss
    Host Vector Type Plasmid
    Host Plasmid Name pCRT7/NT-TOP


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    14 14q13.1 4860     purine nucleoside phosphorylase PNP