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Crystal structure of LSD2-NPAC with H3(1-26)in space group P21
Biology and Chemistry Report
4HSU
  •   Structure Details   Hide

    Structure Keywords

    Keywords OXIDOREDUCTASE
    Text histone demethylase, OXIDOREDUCTASE

    Polymeric Molecules

    Chain A
    Description Lysine-specific histone demethylase 1B 
    Fragment UNP residues 51-822 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 87052.2 
    Source Method genetically manipulated  
    Entity Name LSD2, Flavin-containing amine oxidase domain-containing protein 1, Lysine-specific histone demethylase 2 
    Chain B
    Description Putative oxidoreductase GLYR1 
    Fragment UNP residues 152-268 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13528.4 
    Source Method genetically manipulated  
    Entity Name NPAC, 3-hydroxyisobutyrate dehydrogenase-like protein, Cytokine-like nuclear factor N-PAC, Glyoxylate reductase 1 homolog, Nuclear protein NP60, Nuclear protein of 60 kDa 
    Chain C
    Description Histone H3 
    Fragment UNP residues 2-31 
    Mutation K4M 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 3177.8 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    FAD  FLAVIN-ADENINE DINUCLEOTIDE  C27 H33 N9 O15 P2   785.55  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A KDM1B_HUMAN A2A2C5     
    B GLYR1_HUMAN B4DL47     
    C Q92133_XENLA Q92133     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    1      
    1      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6349   Regulation of Gene Expression by Genetic Imprinting  Heritable Alterations in the Activity of a Gene That Depend On Whether It Passed Through the Paternal or the Maternal Germline But That Are Not Encoded by DNA Itself. 
    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. 
    7275   Multicellular Organismal Development  The Biological Process Whose Specific Outcome Is the Progression of a Multicellular Organism Over Time From an Initial Condition (e.g. a Zygote or a Young Adult) to a Later Condition (e.g. a Multicellular Animal or an Aged Adult). 
    16568   Chromatin Modification  The Alteration of DNA Protein or Sometimes RNA in Chromatin Which May Result in Changing the Chromatin Structure. 
    34720   Histone H3 K4 Demethylation  The Modification of Histone H3 by the Removal of a Methyl Group From Lysine At Position 4 of the Histone. 
    43046   DNA Methylation Involved in Gamete Generation  The Covalent Transfer of a Methyl Group to C 5 of Cytosine That Contributes to the Establishment of DNA Methylation Patterns in the Gamete. 
    44030   Regulation of DNA Methylation  Any Process That Modulates the Frequency Rate or Extent of the Covalent Transfer of a Methyl Group to Either N 6 of Adenine or C 5 or N 4 of Cytosine. 
    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. 
    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. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    8270   Zinc Ion Binding  Interacting Selectively and Non Covalently with Zinc (zn) Ions. 
    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. 
    34648   Histone Demethylase Activity (h3 Dimethyl K4 Specific)  Catalysis of the Removal of a Methyl Group From Dimethylated Lysine At Position 4 of the Histone H3 Protein. 
    34649   Histone Demethylase Activity (h3 Monomethyl K4 Specific)  Catalysis of the Reaction: Histone H3 N6 Methyl L Lysine (position 4) + O2 + FAD + H2o = Histone H3 L Lysine (position 4) + H2o2 + Formaldehyde + Fadh2. This Reaction Is the Removal of a Methyl Group From Monomethylated Lysine At Position 4 of the Histone H3 Protein. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    50660   Flavin Adenine Dinucleotide Binding  Interacting Selectively and Non Covalently with FAD Flavin Adenine Dinucleotide the Coenzyme or the Prosthetic Group of Various Flavoprotein Oxidoreductase Enzymes in Either the Oxidized Form FAD or the Reduced Form Fadh2. 
    Chain B
    GO ID   Ontology GO Term Definition
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    Chain C
    GO ID   Ontology GO Term Definition
    786   Nucleosome  A Complex Comprised of DNA Wound Around a Multisubunit Core and Associated Proteins Which Forms the Primary Packing Unit of DNA Into Higher Order Structures. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene glyr1
    Host Scientific Name Escherichia coli  
    Host Vector Type Plasmid
    Host Plasmid Name pGEX-6P-1


    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene lsd2
    Host Common Name Fall Armyworm
    Host Scientific Name Spodoptera frugiperda  
    Host Cell Line Sf9
    Host Vector Type Baculovirus
    Host Plasmid Name modified pFastBac1


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    6 6p22.3 221656     lysine (K)-specific demethylase 1B KDM1B    
    16 16p13.3 84656     glyoxylate reductase 1 homolog (Arabidopsis) GLYR1