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Co-crystal Structure of Rat DNA polymerase beta Mutator I260Q: Enzyme-DNA-ddTTP
Biology and Chemistry Report
3UXP
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE, LYASE/DNA
    Text pol beta, repair polymerase, BER, TRANSFERASE, LYASE-DNA complex

    Polymeric Molecules

    Chain A,B
    Description DNA polymerase beta 
    Mutation I260Q 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 38404.1 
    Source Method genetically manipulated  
    Chain D,P
    Description DNA 5'-D(P*AP*TP*GP*TP*GP*AP*G)-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 2177.5 
    Source Method synthetic  
    Chain E,T
    Description DNA 5'-D(P*AP*CP*TP*CP*AP*CP*AP*TP*A)-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 2683.8 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    D3T  2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE  C10 H17 N2 O13 P3   466.17  View 
    NA  SODIUM ION  Na   22.99  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B DPOLB_RAT P06766     

    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      
    A B  4.2.99      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    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. 
    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. 
    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. 
    7568   Aging  A Developmental Process That Is a Deterioration and Loss of Function Over Time. Aging Includes Loss of Functions Such As Resistance to Disease Homeostasis and Fertility As Well As Wear and Tear. Aging Includes Cellular Senescence But Is More Inclusive. May Precede Death (go:0016265) and May Succeed Developmental Maturation (go:0021700). 
    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. 
    10332   Response to Gamma Radiation  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 a Gamma Radiation Stimulus. Gamma Radiation Is a Form of Electromagnetic Radiation (emr) or Light Emission of a Specific Frequency Produced From Sub Atomic Particle Interaction Such As Electron Positron Annihilation and Radioactive Decay. Gamma Rays Are Generally Characterized As Emr Having the Highest Frequency and Energy and Also the Shortest Wavelength Within the Electromagnetic Radiation Spectrum. 
    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. 
    55093   Response to Hyperoxia  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 a Stimulus Indicating Increased Oxygen Tension. 
    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. 
    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,B
    Common Name Rat
    Scientific Name Rattus norvegicus  
    Gene polb
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    16 16q12.5 29240     polymerase (DNA directed), beta POLB