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Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with duplex DNA, dGTP and Calcium
Biology and Chemistry Report
4DSJ
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE/DNA
    Text DNA polymerase, polymerization fidelity, calcium cation, pyrophosphorolysis, purine selectivity, blunt end extension, base stacking, DNA synthesis, TRANSFERASE-DNA complex

    Polymeric Molecules

    Chain A,B
    Description DNA polymerase 
    Fragment RESIDUES 298-876 
    Mutation A598D 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 66102.5 
    Source Method genetically manipulated  
    Chain C,E
    Description DNA 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 3687.5 
    Source Method synthetic  
    Chain D,F
    Description dGTP 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 3021.0 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CA  CALCIUM ION  Ca   40.08  View 
    DGT  2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE  C10 H16 N5 O13 P3   507.18  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B E1C9K5_GEOSE E1C9K5     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  2.7.7.7      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    6139   Nucleobase Containing Compound Metabolic Process  Any Cellular Metabolic Process Involving Nucleobases Nucleosides Nucleotides and Nucleic Acids. 
    6260   DNA Replication  The Cellular Metabolic Process in Which a Cell Duplicates One or More Molecules of Dna. DNA Replication Begins When Specific Sequences Known As Origins of Replication Are Recognized and Bound by Initiation Proteins and Ends When the Original DNA Molecule Has Been Completely Duplicated and the Copies Topologically Separated. the Unit of Replication Usually Corresponds to the Genome of the Cell an Organelle or a Virus. the Template For Replication Can Either Be an Existing DNA Molecule or Rna. 
    6261   DNA Dependent DNA Replication  A DNA Replication Process That Uses Parental DNA As a Template For the DNA Dependent DNA Polymerases That Synthesize the New Strands. 
    71897   DNA Biosynthetic Process  The Cellular DNA Metabolic Process Resulting in the Formation of DNA Deoxyribonucleic Acid One of the Two Main Types of Nucleic Acid Consisting of a Long Unbranched Macromolecule Formed From One or Two Strands of Linked Deoxyribonucleotides the 3' Phosphate Group of Each Constituent Deoxyribonucleotide Being Joined in 3' 5' Phosphodiester Linkage to the 5' Hydroxyl Group of the Deoxyribose Moiety of the Next One. 
    90305   Nucleic Acid Phosphodiester Bond Hydrolysis  The Nucleic Acid Metabolic Process in Which the Phosphodiester Bonds Between Nucleotides Are Cleaved by Hydrolysis. 
    3676   Nucleic Acid Binding  Interacting Selectively and Non Covalently with Any Nucleic Acid. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    3887   DNA Directed DNA Polymerase Activity  Catalysis of the Reaction: Deoxynucleoside Triphosphate + Dna(n) = Diphosphate + Dna(n+1); the Synthesis of DNA From Deoxyribonucleotide Triphosphates in the Presence of a DNA Template and a 3'hydroxyl Group. 
    8408   3' 5' Exonuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Nucleic Acids by Removing Nucleotide Residues From the 3' End. 
    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. 
    16779   Nucleotidyltransferase Activity  Catalysis of the Transfer of a Nucleotidyl Group to a Reactant. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Scientific Name Geobacillus stearothermophilus  
    Gene dpo1
    Host Scientific Name Escherichia coli  
    Host Strain Bl21 (de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET28