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Crystal structure of S. pombe Ubiquitin activating enzyme 1 (Uba1) in complex with ubiquitin and ATP/Mg
Biology and Chemistry Report
4II3
  •   Structure Details   Hide

    Structure Keywords

    Keywords LIGASE
    Text Rossmann-like Fold, ubiquitin-like fold, Ubiquitin activating enzyme activity, ATP binding, Ligase activity, ATP/Mg binding, Ubiquitin E2 binding, LIGASE

    Polymeric Molecules

    Chain A,C
    Description Ubiquitin-activating enzyme E1 1 
    Fragment Uba1, UNP residues 13-1012 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 111765.0 
    Source Method genetically manipulated  
    Entity Name Poly(A)+ RNA transport protein 3 
    Chain B,D
    Description Ubiquitin-60S ribosomal protein L40 
    Fragment UNP residues 1-76 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 10740.2 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ATP  ADENOSINE-5'-TRIPHOSPHATE  C10 H16 N5 O13 P3   507.18  View 
    CA  CALCIUM ION  Ca   40.08  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,C UBA1_SCHPO O94609     
    B,D RL402_SCHPO P0CH07     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A C  6.3.2.19      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,C
    GO ID   Ontology GO Term Definition
    6406   MRNA Export From Nucleus  The Directed Movement of MRNA From the Nucleus to the Cytoplasm. 
    6464   Cellular Protein Modification Process  The Covalent Alteration of One or More Amino Acids Occurring in Proteins Peptides and Nascent Polypeptides (co Translational Post Translational Modifications) Occurring At the Level of an Individual Cell. Includes the Modification of Charged Trnas That Are Destined to Occur in a Protein (pre Translation Modification). 
    16567   Protein Ubiquitination  The Process in Which One or More Ubiquitin Groups Are Added to a Protein. 
    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. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    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. 
    3824   Catalytic Activity  Catalysis of a Biochemical Reaction At Physiological Temperatures. in Biologically Catalyzed Reactions the Reactants Are Known As Substrates and the Catalysts Are Naturally Occurring Macromolecular Substances Known As Enzymes. Enzymes Possess Specific Binding Sites For Substrates and Are Usually Composed Wholly or Largely of Protein But RNA That Has Catalytic Activity (ribozyme) Is Often Also Regarded As Enzymatic. 
    4839   Ubiquitin Activating Enzyme Activity  Catalysis of the Reaction: E1 + Ubiquitin + ATP > E1 Ubiquitin + AMP + Ppi Where the E1 Ubiquitin Linkage Is a Thioester Bond Between the C Terminal Glycine of Ub and a Sulfhydryl Side Group of an E1 Cysteine Residue. This Is the First Step in a Cascade of Reactions in Which Ubiquitin Is Ultimately Added to a Protein Substrate. 
    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). 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    8641   Small Protein Activating Enzyme Activity  Catalysis of the Activation of Small Proteins Such As Ubiquitin or Ubiquitin Like Proteins Through the Formation of an ATP Dependent High Energy Thiolester Bond. 
    16874   Ligase Activity  Catalysis of the Joining of Two Substances or Two Groups Within a Single Molecule with the Concomitant Hydrolysis of the Diphosphate Bond in ATP or a Similar Triphosphate. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B,D
    Common Name Fission Yeast
    Scientific Name Schizosaccharomyces pombe  
    Strain STRAIN 972 / ATCC 24843
    Gene ubi2
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3) Codon Plus
    Host Vector Type Plasmid
    Host Plasmid Name pET-28


    Chain A,C
    Common Name Fission Yeast
    Scientific Name Schizosaccharomyces pombe  
    Strain 972 / ATCC 24843
    Details N Terminal Smt3 Fusion (ulp Cleavable)
    Gene ptr3, spbc1604.21c, spbc211.09, ubiquitin activating enzyme 1 (uba1)
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3) Codon Plus
    Host Vector Type Plasmid
    Host Plasmid Name pSMT3


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    II - 2540744     ubiquitin activating enzyme E1 PTR3    
    I - 2541768     ubiquitin-60S ribosomal protein L40 fusion protein UBI1    
    I - 2542428     ubiquitin-60S ribosomal protein L40 fusion protein UEP1