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Crystal structure of Ubiquitin activating enzyme 1 (Uba1) in complex with the Ub E2 Ubc4, ubiquitin, and ATP/Mg
Biology and Chemistry Report
4II2
  •   Structure Details   Hide

    Structure Keywords

    Keywords LIGASE
    Text ubiquitin, E1, E2, Uba1, Ubc4, conformational change, thioester, adenylation, thioester transfer (transthioesterification), ATP-binding, Rossmann-like Fold, ubiquitin-like fold, Ligase activity, ATP/Mg binding, Ubiquitin E2 binding, ubiquitination, nucleus, LIGASE

    Polymeric Molecules

    Chain A
    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
    Description Ubiquitin-60S ribosomal protein L40 
    Fragment UNP residues 1-76 
    Mutation K6R/K11R/K27R/S28A/K29R/K33R/K48R/S57A/K63R 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 9693.0 
    Source Method genetically manipulated  
    Chain C
    Description Ubiquitin-conjugating enzyme E2 4 
    Mutation C21S/C107S 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 18185.6 
    Source Method genetically manipulated  
    Entity Name Ubiquitin carrier protein 4, Ubiquitin-protein ligase 4 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ATP  ADENOSINE-5'-TRIPHOSPHATE  C10 H16 N5 O13 P3   507.18  View 
    EDO  1,2-ETHANEDIOL  C2 H6 O2   62.07  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    PG0  2-(2-METHOXYETHOXY)ETHANOL  C5 H12 O3   120.15  View 
    SO4  SULFATE ION  O4 S   96.06  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A UBA1_SCHPO O94609     
    B RL402_SCHPO P0CH07     
    C UBC4_SCHPO P46595     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    6.3.2.19      
    6.3.2.19      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    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. 
    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. 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    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. 
    Chain C
    GO ID   Ontology GO Term Definition
    209   Protein Polyubiquitination  Addition of Multiple Ubiquitin Groups to a Protein Forming a Ubiquitin Chain. 
    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. 
    4842   Ubiquitin Protein Transferase Activity  Catalysis of the Transfer of Ubiquitin From One Protein to Another Via the Reaction X Ub + Y > Y Ub + X Where Both X Ub and Y Ub Are Covalent Linkages. 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    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 C
    Common Name Fission Yeast
    Scientific Name Schizosaccharomyces pombe  
    Strain 972 / ATCC 24843
    Details C Term His Tag
    Gene spbc119.02, ubc4, ubiquitin conjugating enzyme 4 (ubc4)
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3) Codon Plus
    Host Vector Type Plasmid
    Host Plasmid Name pET-29


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


    Chain A
    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    
    II - 2540083     ubiquitin conjugating enzyme Ubc4 UBC4    
    I - 2541768     ubiquitin-60S ribosomal protein L40 fusion protein UBI1    
    I - 2542428     ubiquitin-60S ribosomal protein L40 fusion protein UEP1