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Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP
Biology and Chemistry Report
4FYD
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE/DNA
    Text DNA polymerase, DNA replication, TRANSFERASE-DNA complex

    Polymeric Molecules

    Chain A,B
    Description DNA polymerase alpha catalytic subunit A 
    Fragment Polymerase domain, UNP residues 349-1258 
    Mutation R508A, N509A, D998N 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 103402.0 
    Source Method genetically manipulated  
    Chain C,D
    Description DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 7628.0 
    Source Method synthetic  
    Chain E,F
    Description DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide/polyribonucleotide hybrid 
    Formula Weight 3929.5 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    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 DPOA_YEAST D6W177     

    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. 
    6270   DNA Replication Initiation  The Process in Which DNA Dependent DNA Replication Is Started; This Involves the Separation of a Stretch of the DNA Double Helix the Recruitment of DNA Polymerases and the Initiation of Polymerase Action. 
    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. 
    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. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain ATCC 204508 / S288C
    Gene cdc17, n2181, pol1, ynl102w
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)rosetta2
    Host Vector Type Plasmid
    Host Plasmid Name pRSFDuet-1


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    XIV - 855621     DNA-directed DNA polymerase alpha catalytic subunit POL1 POL1