An Information Portal to 111749 Biological Macromolecular Structures

Human topoisomerase IIbeta in complex with DNA and etoposide
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Text TOPRIM domain, winged-helix domain, coiled-coil domain, DNA binding and cleavage, nucleus, ISOMERASE-DNA-ISOMERASE INHIBITOR complex

    Polymeric Molecules

    Chain A,B
    Description DNA topoisomerase 2-beta 
    Fragment hTOP2beta cleavage core, UNP residues 450-1206 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 91929.2 
    Source Method genetically manipulated  
    Entity Name DNA topoisomerase II, beta isozyme 
    Chain C,E
    Description DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 2436.6 
    Source Method synthetic  
    Chain D,F
    Description DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 3654.4 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    EVP  (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside  C29 H32 O13   588.56  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B TOP2B_HUMAN Q02880     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    6259   DNA Metabolic Process  Any Cellular Metabolic Process Involving Deoxyribonucleic Acid. This Is One of the Two Main Types of Nucleic Acid Consisting of a Long Unbranched Macromolecule Formed From One or More Commonly Two Strands of Linked Deoxyribonucleotides. 
    6265   DNA Topological Change  The Process in Which a Transformation Is Induced in the Topological Structure of a Double Stranded DNA Helix Resulting in a Change in Linking Number. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    3918   DNA topoisomerase type II (ATP-hydrolyzing) activity  Catalysis of a DNA Topological Transformation by Transiently Cleaving a Pair of Complementary DNA Strands to Form a Gate Through Which a Second Double Stranded DNA Segment Is Passed After Which the Severed Strands in the First DNA Segment Are Rejoined; Product Release Is Coupled to ATP Binding and Hydrolysis; Changes the Linking Number in Multiples of 2. 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    8301   DNA Binding Bending  The Activity of Binding Selectively and Non Covalently to and Distorting the Original Structure of DNA Typically a Straight Helix Into a Bend or Increasing the Bend If the Original Structure Was Intrinsically Bent Due to Its Sequence. 

    Protein Analyses

    Measured Binding Affinities   

  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene top2b
    Host Scientific Name Escherichia coli  
    Host Strain Bl21star(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET51b

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    3 3p24 7155     topoisomerase (DNA) II beta TOP2B    

    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
    rs202152951 LS-SNP   dbSNP   A 454 I - > V Coil 16% (Intermediate) 3 25672322
    rs200930765 LS-SNP   dbSNP   A 746 L - > I Helix 0% (Buried) 3 25666268
    rs188724401 LS-SNP   dbSNP   A 977 H - > L Coil 25% (Intermediate) 3 25661471
    rs75813619 LS-SNP   dbSNP   A 1054 V - > L Helix 35% (Intermediate) 3 25660229
    rs200043349 LS-SNP   dbSNP   A 1166 R - > Q Helix 60% (Exposed) 3 25656775