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Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus V713P mutant bound to G:dCTP
Biology and Chemistry Report
3HT3
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE/DNA
    Text protein-DNA complex, DNA polymerase I, DNA replication, DNA-binding, DNA-directed DNA polymerase, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase, TRANSFERASE-DNA COMPLEX

    Polymeric Molecules

    Chain A,D
    Description DNA polymerase I, large fragment 
    Fragment Residues 298-876 
    Mutation D598A, V713P 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 66056.4 
    Source Method genetically manipulated  
    Chain B,E
    Description 5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 2684.8 
    Source Method synthetic  
    Chain C,F
    Description 5'-D(*AP*CP*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 3703.5 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    DCP  2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE  C9 H16 N3 O13 P3   467.16  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    SO4  SULFATE ION  O4 S   96.06  View 
    SUC  SUCROSE  C12 H22 O11   342.30  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,D D9N168_GEOSE D9N168     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A D  2.7.7.7      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,D
    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. 
    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. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,D
    Scientific Name Geobacillus stearothermophilus  
    Details Isolate From Idaho Hot Spring
    Gene dpo1
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET30a