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Crystal structure of human Ap4A hydrolase
Biology and Chemistry Report
3U53
  •   Structure Details   Hide

    Structure Keywords

    Keywords Hydrolase
    Text Hydrolase

    Polymeric Molecules

    Chain A,B,C,D
    Description Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical] 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 17922.5 
    Source Method genetically manipulated  
    Entity Name asymmetrical diadenosine tetraphosphate hydrolase, Ap4A hydrolase, Ap4Aase, Nudix hydrolase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    SO4  SULFATE ION  O4 S   96.06  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D AP4A_HUMAN D3DRM0     

    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  3.6.1.17      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D
    GO ID   Ontology GO Term Definition
    6915   Apoptotic Process  A Programmed Cell Death Process Which Begins When a Cell Receives an Internal (e.g. DNA Damage) or External Signal (e.g. an Extracellular Death Ligand) and Proceeds Through a Series of Biochemical Events (signaling Pathway Phase) Which Trigger an Execution Phase. the Execution Phase Is the Last Step of an Apoptotic Process and Is Typically Characterized by Rounding Up of the Cell Retraction of Pseudopodes Reduction of Cellular Volume (pyknosis) Chromatin Condensation Nuclear Fragmentation (karyorrhexis) Plasma Membrane Blebbing and Fragmentation of the Cell Into Apoptotic Bodies. When the Execution Phase Is Completed the Cell Has Died. 
    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. 
    4081   Bis(5' Nucleosyl) Tetraphosphatase (asymmetrical) Activity  Catalysis of the Reaction: P(1) P(4) Bis(5' Nucleosyl)tetraphosphate + H2o = Ntp + Nmp. Acts On Bis(5' Guanosyl) Bis(5' Xanthosyl) Bis(5' Adenosyl) and Bis(5' Uridyl) Tetraphosphate. 
    5525   GTP Binding  Interacting Selectively and Non Covalently with GTP Guanosine Triphosphate. 
    16787   Hydrolase Activity  Catalysis of the Hydrolysis of Various Bonds E.g. C O C N C C Phosphoric Anhydride Bonds Etc. Hydrolase Is the Systematic Name For Any Enzyme of EC Class 3. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C,D
    Common Name Human
    Scientific Name Homo sapiens  
    Gene nudt2
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET22b


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    9 9p13 318     nudix (nucleoside diphosphate linked moiety X)-type motif 2 NUDT2    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs141924472 LS-SNP   dbSNP   A 23 A - > S Bend 48% (Exposed) 9 34339104
    rs190610008 LS-SNP   dbSNP   A 25 E - > V Beta Ladder 14% (Intermediate) 9 34339111
    rs201292035 LS-SNP   dbSNP   A 30 Q - > R Beta Ladder 17% (Intermediate) 9 34339126
    rs199838637 LS-SNP   dbSNP   A 31 A - > T Beta Ladder 16% (Intermediate) 9 34339128
    rs150256259 LS-SNP   dbSNP   A 67 A - > T 3/10 Helix 63% (Exposed) 9 34343193
    rs200364521 LS-SNP   dbSNP   A 96 A - > G Beta Ladder 0% (Buried) 9 34343281
    rs200001373 LS-SNP   dbSNP   A 97 E - > G Beta Ladder 22% (Intermediate) 9 34343284
    rs139349384 LS-SNP   dbSNP   A 103 V - > M Coil 10% (Intermediate) 9 34343301
    rs143347739 LS-SNP   dbSNP   A 115 R - > C Beta Ladder 59% (Exposed) 9 34343337
    rs147348519 LS-SNP   dbSNP   A 123 C - > R Helix 6% (Buried) 9 34343361
    rs139419109 LS-SNP   dbSNP   A 124 Q - > H Helix 73% (Exposed) 9 34343366