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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     

    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
    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. 
    19941   Modification Dependent Protein Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of a Protein or Peptide by Hydrolysis of Its Peptide Bonds Initiated by the Covalent Modification of the Target 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. 
    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. 
    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. 
    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. 
    Chain C
    GO ID   Ontology GO Term Definition
    70   Mitotic Sister Chromatid Segregation  The Cell Cycle Process in Which Replicated Homologous Chromosomes Are Organized and Then Physically Separated and Apportioned to Two Sets During the Mitotic Cell Cycle. Each Replicated Chromosome Composed of Two Sister Chromatids Aligns At the Cell Equator Paired with Its Homologous Partner. One Homolog of Each Morphologic Type Goes Into Each of the Resulting Chromosome Sets. 
    209   Protein Polyubiquitination  Addition of Multiple Ubiquitin Groups to a Protein Forming a Ubiquitin Chain. 
    16485   Protein Processing  Any Protein Maturation Process Achieved by the Cleavage of a Peptide Bond or Bonds Within a Protein. Protein Maturation Is the Process Leading to the Attainment of the Full Functional Capacity of a Protein. 
    16567   Protein Ubiquitination  The Process in Which One or More Ubiquitin Groups Are Added to a Protein. 
    31146   Scf Dependent Proteasomal Ubiquitin Dependent Protein Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of a Protein or Peptide by Hydrolysis of Its Peptide Bonds Initiated by the Covalent Attachment of Ubiquitin with Ubiquitin Protein Ligation Catalyzed by an Scf (skp1/cul1/f Box Protein) Complex and Mediated by the Proteasome. 
    42787   Protein Ubiquitination Involved in Ubiquitin Dependent Protein Catabolic Process  The Process in Which a Ubiquitin Group or Multiple Groups Are Covalently Attached to the Target Protein Thereby Initiating the Degradation of That Protein. 
    45842   Positive Regulation of Mitotic Metaphase/anaphase Transition  Any Process That Activates or Increases the Frequency Rate or Extent of the Mitotic Metaphase to Anaphase Transition. 
    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. 
    43224   Nuclear Scf Ubiquitin Ligase Complex  A Ubiquitin Ligase Complex Located in the Nucleus in Which a Cullin From the Cul1 Subfamily and a Ring Domain Protein Form the Catalytic Core; Substrate Specificity Is Conferred by a Skp1 Adaptor and an F Box Protein. Scf Complexes Are Involved in Targeting Proteins For Degradation by the Proteasome. the Best Characterized Complexes Are Those From Yeast and Mammals (with Core Subunits Named Cdc53/cul1 Rbx1/hrt1/roc1). 
    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. 
    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. 
    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. 
    61631   Ubiquitin Conjugating Enzyme Activity  Isoenergetic Transfer of Ubiquitin From One Protein to Another Via the Reaction X Ubiquitin + Y > Y Ubiquitin + X Where Both the X Ubiquitin and Y Ubiquitin Linkages Are Thioester Bonds Between the C Terminal Glycine of Ubiquitin and a Sulfhydryl Side Group of a Cysteine Residue. 
    90302   Apc Cdc20 Complex Activity  A Ubiquitin Protein Ligase Activity That Increases the Rate or Extent of the Metaphase to Anaphase Transition of the Mitotic Cell Cycle. 


     
  •   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