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Open ternary complex of R283K DNA polymerase beta with a one metal bound dCTP analog
Biology and Chemistry Report
4F5O
  •   Structure Details   Hide

    Structure Keywords

    Keywords Transferase, Lyase/DNA
    Text Transferase, Lyase/DNA, Lyase-DNA complex

    Polymeric Molecules

    Chain A
    Description DNA polymerase beta 
    Mutation R283K 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 38214.0 
    Source Method genetically manipulated  
    Chain T
    Description DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 4860.2 
    Source Method synthetic  
    Chain P
    Description DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 3085.1 
    Source Method synthetic  
    Chain D
    Description DNA (5'-D(P*GP*TP*CP*GP*G)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 1536.1 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    6CF  2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine  C10 H16 F2 N3 O12 P3   501.17  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A DPOLB_HUMAN B2RC78     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    2.7.7.7      
    4.2.99      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    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. 
    6281   DNA Repair  The Process of Restoring DNA After Damage. Genomes Are Subject to Damage by Chemical and Physical Agents in the Environment (e.g. Uv and Ionizing Radiations Chemical Mutagens Fungal and Bacterial Toxins Etc.) and by Free Radicals or Alkylating Agents Endogenously Generated in Metabolism. DNA Is Also Damaged Because of Errors During Its Replication. a Variety of Different DNA Repair Pathways Have Been Reported That Include Direct Reversal Base Excision Repair Nucleotide Excision Repair Photoreactivation Bypass Double Strand Break Repair Pathway and Mismatch Repair Pathway. 
    6974   Cellular Response to DNA Damage Stimulus  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Stimulus Indicating Damage to Its DNA From Environmental Insults or Errors During Metabolism. 
    5634   Nucleus  A Membrane Bounded Organelle of Eukaryotic Cells in Which Chromosomes Are Housed and Replicated. in Most Cells the Nucleus Contains All of the Cell's Chromosomes Except the Organellar Chromosomes and Is the Site of RNA Synthesis and Processing. in Some Species or in Specialized Cell Types RNA Metabolism or DNA Replication May Be Absent. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    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. 
    5515   Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    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. 
    16829   Lyase Activity  Catalysis of the Cleavage of C C C O C N and Other Bonds by Other Means Than by Hydrolysis or Oxidation or Conversely Adding a Group to a Double Bond. They Differ From Other Enzymes in That Two Substrates Are Involved in One Reaction Direction But Only One in the Other Direction. When Acting On the Single Substrate a Molecule Is Eliminated and This Generates Either a New Double Bond or a New Ring. 
    19899   Enzyme Binding  Interacting Selectively and Non Covalently with Any Enzyme. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene polb
    Host Scientific Name Escherichia coli  
    Host Strain Tap56
    Host Vector Type Plasmid
    Host Plasmid Name pWL11


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    8 8p11.2 5423     polymerase (DNA directed), beta POLB    

    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
    rs149565363 LS-SNP   dbSNP   A 30 S - > N Bend 59% (Exposed) 8 42196557
    rs111586415 LS-SNP   dbSNP   A 52 K - > E Coil 65% (Exposed) 8 42202505
    rs79251622 LS-SNP   dbSNP   A 54 K - > T Coil 83% (Exposed) 8 42202512
    rs147215490 LS-SNP   dbSNP   A 71 E - > G Helix 61% (Exposed) 8 42206559
    rs201913498 LS-SNP   dbSNP   A 83 R - > C Helix 78% (Exposed) 8 42206594
    rs148674351 LS-SNP   dbSNP   A 98 N - > S Helix 21% (Intermediate) 8 42207556
    rs12678588 LS-SNP   dbSNP   A 137 R - > Q Helix 37% (Exposed) 8 42213073
    rs10091081 LS-SNP   dbSNP   A 144 G - > A Helix 54% (Exposed) 8 42214695
    rs200554507 LS-SNP   dbSNP   A 149 R - > G Coil 56% (Exposed) 8 42214709 6CF,MG
    rs56121607 LS-SNP   dbSNP   A 196 T - > S Beta Ladder 0% (Buried) 8 42218849
    rs149882093 LS-SNP   dbSNP   A 236 M - > T Beta Ladder 19% (Intermediate) 8 42220215
    rs3136797 LS-SNP   dbSNP   A 242 P - > R Coil 67% (Exposed) 8 42226805
    rs184348926 LS-SNP   dbSNP   A 255 I - > V Beta Ladder 0% (Buried) 8 42226843
    rs139801051 LS-SNP   dbSNP   A 259 L - > S Beta Ladder 8% (Buried) 8 42227369
    rs141666437 LS-SNP   dbSNP   A 271 Y - > C Helix 37% (Exposed) 8 42227405 6CF,MG
    rs146877435 LS-SNP   dbSNP   A 328 R - > Q Coil 28% (Intermediate) 8 42229150
    rs200881222 LS-SNP   dbSNP   A 334 S - > R Coil 64% (Exposed) 8 42229169
    rs200653703 LS-SNP   dbSNP   A 335 E - > K Coil 63% (Exposed) 8 42229170