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Crystal structure of mouse DXO in complex with substrate mimic RNA and calcium ion
Biology and Chemistry Report
4J7M
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/RNA
    Text Decapping, 5'-3' exoribonuclease, HYDROLASE, HYDROLASE-RNA complex

    Polymeric Molecules

    Chain A
    Description Protein Dom3Z 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 43132.9 
    Source Method genetically manipulated  
    Entity Name Dom-3 homolog Z, DXO 
    Chain B
    Description RNA (5'-R(P*UP*(U37)P*(U37)P*UP*U)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polyribonucleotide 
    Formula Weight 1518.0 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CA  CALCIUM ION  Ca   40.08  View 
    UBD  URIDINE 3',5'-BIS(DIHYDROGEN PHOSPHATE)  C9 H14 N2 O12 P2   404.16  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A DXO_MOUSE O70348     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    3.1.13      
    3.6.1      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6402   MRNA Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of MRNA Messenger RNA Which Is Responsible For Carrying the Coded Genetic 'message' Transcribed From DNA to Sites of Protein Assembly At the Ribosomes. 
    8152   Metabolic Process  The Chemical Reactions and Pathways Including Anabolism and Catabolism by Which Living Organisms Transform Chemical Substances. Metabolic Processes Typically Transform Small Molecules But Also Include Macromolecular Processes Such As DNA Repair and Replication and Protein Synthesis and Degradation. 
    50779   RNA Destabilization  Any Process That Decreases the Stability of an RNA Molecule Making It More Vulnerable to Degradative Processes. 
    71028   Nuclear MRNA Surveillance  The Set of Processes Involved in Identifying and Degrading Defective or Aberrant Mrnas Within the Nucleus. 
    90305   Nucleic Acid Phosphodiester Bond Hydrolysis  The Nucleic Acid Metabolic Process in Which the Phosphodiester Bonds Between Nucleotides Are Cleaved by Hydrolysis. 
    5575   Cellular_component  The Part of a Cell or Its Extracellular Environment in Which a Gene Product Is Located. a Gene Product May Be Located in One or More Parts of a Cell and Its Location May Be As Specific As a Particular Macromolecular Complex That Is a Stable Persistent Association of Macromolecules That Function Together. 
    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. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    287   Magnesium Ion Binding  Interacting Selectively and Non Covalently with Magnesium (mg) Ions. 
    3723   RNA Binding  Interacting Selectively and Non Covalently with an RNA Molecule or a Portion Thereof. 
    3729   MRNA Binding  Interacting Selectively and Non Covalently with Messenger RNA (mrna) an Intermediate Molecule Between DNA and Protein. MRNA Includes Utr and Coding Sequences But Does Not Contain Introns. 
    4518   Nuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Nucleic Acids. 
    4527   Exonuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Nucleic Acids by Removing Nucleotide Residues From the 3' or 5' End. 
    8409   5' 3' Exonuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Nucleic Acids by Removing Nucleotide Residues From the 5' End. 
    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. 
    34353   RNA Pyrophosphohydrolase Activity  Catalysis of the Removal of a 5' Terminal Pyrophosphate From the 5' Triphosphate End of an RNA Leaving a 5' Monophosphate End. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Mouse
    Scientific Name Mus musculus  
    Gene dom3z, ng6
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    17 17 B1|17 112403     decapping exoribonuclease DXO