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DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR), MGCL2 (5 MILLIMOLAR), AND MNCL2 (5 MILLIMOLAR)
Biology and Chemistry Report
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  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE/DNA
    Text DNA-DIRECTED DNA POLYMERASE, DNA REPLICATION, DNA REPAIR, NUCLEOTIDYLTRANSFERASE, COMPLEX (NUCLEOTIDYLTRANSFERASE-DNA, TRANSFERASE-DNA complex

    Polymeric Molecules

    Chain T
    Description DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 2434.7 
    Source Method synthetic  
    Chain P
    Description DNA (5'-D(*TP*CP*TP*AP*AP*TP*GP*A)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 2425.7 
    Source Method synthetic  
    Chain A
    Description PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7)) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 38242.1 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    DTP  2'-DEOXYADENOSINE 5'-TRIPHOSPHATE  C10 H16 N5 O12 P3   491.18  View 
    MN  MANGANESE (II) ION  Mn   54.94  View 
    NA  SODIUM ION  Na   22.99  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 Catalytic Site(s)
    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. 
    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. 
    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. 
    6284   Base Excision Repair  In Base Excision Repair an Altered Base Is Removed by a DNA Glycosylase Enzyme Followed by Excision of the Resulting Sugar Phosphate. the Small Gap Left in the DNA Helix Is Filled in by the Sequential Action of DNA Polymerase and DNA Ligase. 
    6287   Base Excision Repair Gap Filling  Repair of the Damaged Strand by the Combined Action of an Apurinic Endouclease That Degrades a Few Bases On the Damaged Strand and a Polymerase That Synthesizes a 'patch' in the 5' to 3' Direction Using the Undamaged Strand As a Template. 
    6290   Pyrimidine Dimer Repair  The Repair of Uv Induced T T C T and C C Dimers. 
    6297   Nucleotide Excision Repair DNA Gap Filling  Repair of the Gap in the DNA Helix by DNA Polymerase and DNA Ligase After the Portion of the Strand Containing the Lesion Has Been Removed by Pyrimidine Dimer Repair Enzymes. 
    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. 
    8630   Intrinsic Apoptotic Signaling Pathway in Response to DNA Damage  A Series of Molecular Signals in Which an Intracellular Signal Is Conveyed to Trigger the Apoptotic Death of a Cell. the Pathway Is Induced by the Detection of DNA Damage and Ends When the Execution Phase of Apoptosis Is Triggered. 
    45471   Response to Ethanol  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of an Ethanol Stimulus. 
    51402   Neuron Apoptotic Process  Any Apoptotic Process in a Neuron the Basic Cellular Unit of Nervous Tissue. Each Neuron Consists of a Body an Axon and Dendrites. Their Purpose Is to Receive Conduct and Transmit Impulses in the Nervous System. 
    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. 
    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. 
    5654   Nucleoplasm  That Part of the Nuclear Content Other Than the Chromosomes or the Nucleolus. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5874   Microtubule  Any of the Long Generally Straight Hollow Tubes of Internal Diameter 12 15 Nm and External Diameter 24 Nm Found in a Wide Variety of Eukaryotic Cells; Each Consists (usually) of 13 Protofilaments of Polymeric Tubulin Staggered in Such a Manner That the Tubulin Monomers Are Arranged in a Helical Pattern On the Microtubular Surface and with the Alpha/beta Axes of the Tubulin Subunits Parallel to the Long Axis of the Tubule; Exist in Equilibrium with Pool of Tubulin Monomers and Can Be Rapidly Assembled or Disassembled in Response to Physiological Stimuli; Concerned with Force Generation E.g. in the Spindle. 
    5876   Spindle Microtubule  Any Microtubule That Is Part of a Mitotic or Meiotic Spindle; Anchored At One Spindle Pole. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    3684   Damaged DNA Binding  Interacting Selectively and Non Covalently with Damaged Dna. 
    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). 
    8017   Microtubule Binding  Interacting Selectively and Non Covalently with Microtubules Filaments Composed of Tubulin Monomers. 
    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. 
    34061   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 Nucleic Acid Template and a 3'hydroxyl Group. 
    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  
    Genus Homo
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia


    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 25% (Intermediate) 8 42196557
    rs111586415 LS-SNP   dbSNP   A 52 K - > E Coil 59% (Exposed) 8 42202505
    rs79251622 LS-SNP   dbSNP   A 54 K - > T Coil 68% (Exposed) 8 42202512
    rs147215490 LS-SNP   dbSNP   A 71 E - > G Helix 71% (Exposed) 8 42206559
    rs201913498 LS-SNP   dbSNP   A 83 R - > C Helix 66% (Exposed) 8 42206594
    rs148674351 LS-SNP   dbSNP   A 98 N - > S Helix 43% (Exposed) 8 42207556
    rs12678588 LS-SNP   dbSNP   A 137 R - > Q Helix 40% (Exposed) 8 42213073
    rs10091081 LS-SNP   dbSNP   A 144 G - > A Helix 45% (Exposed) 8 42214695
    rs200554507 LS-SNP   dbSNP   A 149 R - > G Coil 58% (Exposed) 8 42214709 DTP
    rs56121607 LS-SNP   dbSNP   A 196 T - > S Beta Ladder 0% (Buried) 8 42218849
    rs139070534 LS-SNP   dbSNP   A 208 P - > A Turn 37% (Exposed) 8 42220130
    rs149882093 LS-SNP   dbSNP   A 236 M - > T Beta Ladder 19% (Intermediate) 8 42220215
    rs3136797 LS-SNP   dbSNP   A 242 P - > R Coil 60% (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 5% (Buried) 8 42227369
    rs141666437 LS-SNP   dbSNP   A 271 Y - > C Helix 32% (Intermediate) 8 42227405
    rs146877435 LS-SNP   dbSNP   A 328 R - > Q Coil 17% (Intermediate) 8 42229150
    rs200881222 LS-SNP   dbSNP   A 334 S - > R Turn 55% (Exposed) 8 42229169
    rs200653703 LS-SNP   dbSNP   A 335 E - > K Coil 73% (Exposed) 8 42229170