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Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+
Biology and Chemistry Report
4IEM
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE, LYASE/DNA
    Text metalloprotein, DNA damage, DNA repair, base excision repair, protein-DNA, REF1, nuclease, HYDROLASE, LYASE-DNA complex

    Polymeric Molecules

    Chain A,B,C,D
    Description DNA-(apurinic or apyrimidinic site) lyase 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 35475.6 
    Source Method genetically manipulated  
    Entity Name APEX nuclease, APEN, Apurinic-apyrimidinic endonuclease 1, AP endonuclease 1, APE-1, REF-1, Redox factor-1, DNA-(apurinic or apyrimidinic site) lyase, mitochondrial 
    Chain E,H,K,N
    Description DNA (5'-D(*GP*CP*TP*AP*C)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 1480.0 
    Source Method synthetic  
    Chain F,I,L,O
    Description DNA (5'-D(P*(3DR)P*GP*AP*TP*CP*G)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 1700.2 
    Source Method synthetic  
    Chain G,J,M,P
    Description DNA (5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*C)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 3374.2 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    MG  MAGNESIUM ION  Mg   24.31  View 
    NA  SODIUM ION  Na   22.99  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D APEX1_HUMAN P27695     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B C D  3.1      
    A B C D  4.2.99.18      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D
    GO ID   Ontology GO Term Definition
    737   DNA Catabolic Process Endonucleolytic  The Chemical Reactions and Pathways Resulting in the Breakdown of DNA Involving the Hydrolysis of Internal 3' 5' Phosphodiester Bonds in One or Two Strands of Deoxyribonucleotides. 
    738   DNA Catabolic Process Exonucleolytic  The Chemical Reactions and Pathways Resulting in the Breakdown of DNA Involving the Hydrolysis of Terminal 3' 5' Phosphodiester Bonds in One or Two Strands of Deoxyribonucleotides. 
    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. 
    6310   DNA Recombination  Any Process in Which a New Genotype Is Formed by Reassortment of Genes Resulting in Gene Combinations Different From Those That Were Present in the Parents. in Eukaryotes Genetic Recombination Can Occur by Chromosome Assortment Intrachromosomal Recombination or Nonreciprocal Interchromosomal Recombination. Intrachromosomal Recombination Occurs by Crossing Over. in Bacteria It May Occur by Genetic Transformation Conjugation Transduction or F Duction. 
    6351   Transcription DNA Templated  The Cellular Synthesis of RNA On a Template of Dna. 
    6355   Regulation of Transcription DNA Templated  Any Process That Modulates the Frequency Rate or Extent of Cellular DNA Templated Transcription. 
    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). 
    10243   Response to Organonitrogen Compound  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 Organonitrogen Stimulus. an Organonitrogen Compound Is Formally a Compound Containing At Least One Carbon Nitrogen Bond. 
    14912   Negative Regulation of Smooth Muscle Cell Migration  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Smooth Muscle Cell Migration. 
    42493   Response to Drug  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 Drug Stimulus. a Drug Is a Substance Used in the Diagnosis Treatment or Prevention of a Disease. 
    43488   Regulation of MRNA Stability  Any Process That Modulates the Propensity of MRNA Molecules to Degradation. Includes Processes That Both Stabilize and Destabilize Mrnas. 
    45454   Cell Redox Homeostasis  Any Process That Maintains the Redox Environment of a Cell or Compartment Within a Cell. 
    45739   Positive Regulation of DNA Repair  Any Process That Activates or Increases the Frequency Rate or Extent of DNA Repair. 
    55114   Oxidation Reduction Process  A Metabolic Process That Results in the Removal or Addition of One or More Electrons to or From a Substance with or Without the Concomitant Removal or Addition of a Proton or Protons. 
    70301   Cellular Response to Hydrogen Peroxide  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 Hydrogen Peroxide (h2o2) Stimulus. 
    71320   Cellular Response to Camp  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 Camp (cyclic AMP Adenosine 3' 5' Cyclophosphate) Stimulus. 
    71375   Cellular Response to Peptide Hormone 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 Peptide Hormone Stimulus. a Peptide Hormone Is Any of a Class of Peptides That Are Secreted Into the Blood Stream and Have Endocrine Functions in Living Animals. 
    71417   Cellular Response to Organonitrogen Compound  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 an Organonitrogen Stimulus. an Organonitrogen Compound Is Formally a Compound Containing At Least One Carbon Nitrogen Bond. 
    80111   DNA Demethylation  The Removal of a Methyl Group From One or More Nucleotides Within an DNA Molecule. 
    90502   RNA Phosphodiester Bond Hydrolysis Endonucleolytic  The Chemical Reactions and Pathways Involving the Hydrolysis of Internal 3' 5' Phosphodiester Bonds in One or Two Strands of Ribonucleotides. 
    1900087   Positive Regulation of G1/s Transition of Mitotic Cell Cycle  Any Cell Cycle Regulatory Process That Promotes the Commitment of a Cell From G1 to S Phase of the Mitotic Cell Cycle. 
    1903507   Negative Regulation of Nucleic Acid Templated Transcription  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Nucleic Acid Templated Transcription. 
    5622   Intracellular  The Living Contents of a Cell; the Matter Contained Within (but Not Including) the Plasma Membrane Usually Taken to Exclude Large Vacuoles and Masses of Secretory or Ingested Material. in Eukaryotes It Includes the Nucleus and Cytoplasm. 
    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. 
    5667   Transcription Factor Complex  A Protein Complex That Is Capable of Associating with DNA by Direct Binding or Via Other DNA Binding Proteins or Complexes and Regulating Transcription. 
    5730   Nucleolus  A Small Dense Body One or More of Which Are Present in the Nucleus of Eukaryotic Cells. It Is Rich in RNA and Protein Is Not Bounded by a Limiting Membrane and Is Not Seen During Mitosis. Its Prime Function Is the Transcription of the Nucleolar DNA Into 45s Ribosomal Precursor RNA the Processing of This RNA Into 5.8s 18s and 28s Components of Ribosomal RNA and the Association of These Components with 5s RNA and Proteins Synthesized Outside the Nucleolus. This Association Results in the Formation of Ribonucleoprotein Precursors; These Pass Into the Cytoplasm and Mature Into the 40s and 60s Subunits of the Ribosome. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5739   Mitochondrion  A Semiautonomous Self Replicating Organelle That Occurs in Varying Numbers Shapes and Sizes in the Cytoplasm of Virtually All Eukaryotic Cells. It Is Notably the Site of Tissue Respiration. 
    5783   Endoplasmic Reticulum  The Irregular Network of Unit Membranes Visible Only by Electron Microscopy That Occurs in the Cytoplasm of Many Eukaryotic Cells. the Membranes Form a Complex Meshwork of Tubular Channels Which Are Often Expanded Into Slitlike Cavities Called Cisternae. the Er Takes Two Forms Rough (or Granular) with Ribosomes Adhering to the Outer Surface and Smooth (with No Ribosomes Attached). 
    5813   Centrosome  A Structure Comprised of a Core Structure (in Most Organisms a Pair of Centrioles) and Peripheral Material From Which a Microtubule Based Structure Such As a Spindle Apparatus Is Organized. Centrosomes Occur Close to the Nucleus During Interphase in Many Eukaryotic Cells Though in Animal Cells It Changes Continually During the Cell Division Cycle. 
    5840   Ribosome  An Intracellular Organelle About 200 a in Diameter Consisting of RNA and Protein. It Is the Site of Protein Biosynthesis Resulting From Translation of Messenger RNA (mrna). It Consists of Two Subunits One Large and One Small Each Containing Only Protein and Rna. Both the Ribosome and Its Subunits Are Characterized by Their Sedimentation Coefficients Expressed in Svedberg Units (symbol: S). Hence the Prokaryotic Ribosome (70s) Comprises a Large (50s) Subunit and a Small (30s) Subunit While the Eukaryotic Ribosome (80s) Comprises a Large (60s) Subunit and a Small (40s) Subunit. Two Sites On the Ribosomal Large Subunit Are Involved in Translation Namely the Aminoacyl Site (a Site) and Peptidyl Site (p Site). Ribosomes From Prokaryotes Eukaryotes Mitochondria and Chloroplasts Have Characteristically Distinct Ribosomal Proteins. 
    16607   Nuclear Speck  A Discrete Extra Nucleolar Subnuclear Domain 20 50 in Number in Which Splicing Factors Are Seen to Be Localized by Immunofluorescence Microscopy. 
    48471   Perinuclear Region of Cytoplasm  Cytoplasm Situated Near or Occurring Around the Nucleus. 
    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. 
    3713   Transcription Coactivator Activity  Interacting Selectively and Non Covalently with a Activating Transcription Factor and Also with the Basal Transcription Machinery in Order to Increase the Frequency Rate or Extent of Transcription. Cofactors Generally Do Not Bind the Template Nucleic Acid But Rather Mediate Protein Protein Interactions Between Activating Transcription Factors and the Basal Transcription Machinery. 
    3714   Transcription Corepressor Activity  Interacting Selectively and Non Covalently with a Repressing Transcription Factor and Also with the Basal Transcription Machinery in Order to Stop Prevent or Reduce the Frequency Rate or Extent of Transcription. Cofactors Generally Do Not Bind the Template Nucleic Acid But Rather Mediate Protein Protein Interactions Between Repressive Transcription Factors and the Basal Transcription Machinery. 
    3723   RNA Binding  Interacting Selectively and Non Covalently with an RNA Molecule or a Portion Thereof. 
    3906   DNA-(apurinic or apyrimidinic site) lyase activity  Catalysis of the Cleavage of the C O P Bond 3' to the Apurinic or Apyrimidinic Site in DNA by a Beta Elimination Reaction Leaving a 3' Terminal Unsaturated Sugar and a Product with a Terminal 5' Phosphate. 
    4518   Nuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Nucleic Acids. 
    4519   Endonuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Nucleic Acids by Creating Internal Breaks. 
    4520   Endodeoxyribonuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Deoxyribonucleic Acid by Creating Internal Breaks. 
    4521   Endoribonuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Ribonucleic Acid by Creating Internal Breaks. 
    4523   RNA DNA Hybrid Ribonuclease Activity  Catalysis of the Endonucleolytic Cleavage of RNA in RNA DNA Hybrids to 5' Phosphomonoesters. 
    4527   Exonuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Nucleic Acids by Removing Nucleotide Residues From the 3' or 5' End. 
    4528   Phosphodiesterase I Activity  Catalysis of the Sequential Hydrolytic Removal of 5' Nucleotides From the 3' Hydroxy Termini of 3' Hydroxy Terminated Oligonucleotides. 
    4844   Uracil DNA N Glycosylase Activity  Catalysis of the Cleavage of the N C1' Glycosidic Bond Between the Damaged DNA Base and the Deoxyribose Sugar Releasing a Free Base and Leaving an Apyrimidinic (ap) Site. Enzymes with This Activity Recognize and Remove Uracil Bases in DNA That Result From the Deamination of Cytosine or the Misincorporation of Dutp Opposite an Adenine. 
    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). 
    8081   Phosphoric Diester Hydrolase Activity  Catalysis of the Hydrolysis of a Phosphodiester to Give a Phosphomonoester and a Free Hydroxyl Group. 
    8311   Double Stranded DNA 3' 5' Exodeoxyribonuclease Activity  Catalysis of the Sequential Cleavage of Mononucleotides From a Free 3' Terminus of a Double Stranded DNA Molecule. 
    8408   3' 5' Exonuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Nucleic Acids by Removing Nucleotide Residues From the 3' End. 
    16491   Oxidoreductase Activity  Catalysis of an Oxidation Reduction (redox) Reaction a Reversible Chemical Reaction in Which the Oxidation State of an Atom or Atoms Within a Molecule Is Altered. One Substrate Acts As a Hydrogen or Electron Donor and Becomes Oxidized While the Other Acts As Hydrogen or Electron Acceptor and Becomes Reduced. 
    16787   Hydrolase Activity  Catalysis of the Hydrolysis of Various Bonds E.g. C O C N C C Phosphoric Anhydride Bonds Etc. Hydrolase Is the Systematic Name For Any Enzyme of EC Class 3. 
    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. 
    16890   Site Specific Endodeoxyribonuclease Activity Specific For Altered Base  Catalysis of the Hydrolysis of Ester Linkages At Specific Sites Within a Deoxyribonucleic Acid Molecule by Creating Internal Breaks. 
    31490   Chromatin DNA Binding  Interacting Selectively and Non Covalently with DNA That Is Assembled Into Chromatin. 
    32403   Protein Complex Binding  Interacting Selectively and Non Covalently with Any Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    44822   Poly(a) RNA Binding  Interacting Non Covalently with a Poly(a) RNA a RNA Molecule Which Has a Tail of Adenine Bases. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    51059   Nf Kappab Binding  Interacting Selectively and Non Covalently with Nf Kappab a Transcription Factor For Eukaryotic RNA Polymerase Ii Promoters. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C,D
    Common Name Human
    Scientific Name Homo sapiens  
    Gene ape, ape1, apex, apex1, apx, hap1, ref1
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    14 14q11.2 328     APEX nuclease (multifunctional DNA repair enzyme) 1 APEX1