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Structual basis for the recognition of Ubc13 by the Shigella flexneri effector OspI
Biology and Chemistry Report
3W31
  •   Structure Details   Hide

    Structure Keywords

    Keywords IMMUNE SYSTEM
    Text Type 3 secretion system, Effector, Deamidation, IMMUNE SYSTEM

    Polymeric Molecules

    Chain A
    Description ORF169b 
    Mutation C62A 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 24119.0 
    Source Method genetically manipulated  
    Chain B
    Description Ubiquitin-conjugating enzyme E2 N 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 17440.2 
    Source Method genetically manipulated  
    Entity Name Bendless-like ubiquitin-conjugating enzyme, Ubc13, UbcH13, Ubiquitin carrier protein N, Ubiquitin-protein ligase N 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    IOD  IODIDE ION  I   126.90  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A Q8VSD5_SHIFL Q6XVV4     
    B UBE2N_HUMAN P61088     

    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      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain B
    GO ID   Ontology GO Term Definition
    724   Double Strand Break Repair Via Homologous Recombination  The Error Free Repair of a Double Strand Break in DNA in Which the Broken DNA Molecule Is Repaired Using Homologous Sequences. a Strand in the Broken DNA Searches For a Homologous Region in an Intact Chromosome to Serve As the Template For DNA Synthesis. the Restoration of Two Intact DNA Molecules Results in the Exchange Reciprocal or Nonreciprocal of Genetic Material Between the Intact DNA Molecule and the Broken DNA Molecule. 
    729   DNA Double Strand Break Processing  The 5' to 3' Exonucleolytic Resection of the DNA At the Site of the Break to Form a 3' Single Strand DNA Overhang. 
    2224   Toll Like Receptor Signaling Pathway  Any Series of Molecular Signals Generated As a Consequence of Binding to a Toll Like Receptor. Toll Like Receptors Directly Bind Pattern Motifs From a Variety of Microbial Sources to Initiate Innate Immune Response. 
    2755   Myd88 Dependent Toll Like Receptor Signaling Pathway  Any Series of Molecular Signals Generated As a Consequence of Binding to a Toll Like Receptor Where the Myd88 Adaptor Molecule Mediates Transduction of the Signal. Toll Like Receptors Directly Bind Pattern Motifs From a Variety of Microbial Sources to Initiate Innate Immune Response. 
    6281   DNA Repair  The Process of Restoring DNA After Damage. Genomes Are Subject to Damage by Chemical and Physical Agents in the Environment (e.g. Uv and Ionizing Radiations Chemical Mutagens Fungal and Bacterial Toxins Etc.) and by Free Radicals or Alkylating Agents Endogenously Generated in Metabolism. DNA Is Also Damaged Because of Errors During Its Replication. a Variety of Different DNA Repair Pathways Have Been Reported That Include Direct Reversal Base Excision Repair Nucleotide Excision Repair Photoreactivation Bypass Double Strand Break Repair Pathway and Mismatch Repair Pathway. 
    6282   Regulation of DNA Repair  Any Process That Modulates the Frequency Rate or Extent of DNA Repair. 
    6301   Postreplication Repair  The Conversion of DNA Damage Induced Single Stranded Gaps Into Large Molecular Weight DNA After Replication. Includes Pathways That Remove Replication Blocking Lesions in Conjunction with DNA Replication. 
    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). 
    6508   Proteolysis  The Hydrolysis of Proteins Into Smaller Polypeptides And/or Amino Acids by Cleavage of Their Peptide Bonds. 
    6511   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 a Ubiquitin Group or Multiple Ubiquitin Groups to the Protein. 
    6974   Cellular Response to DNA Damage Stimulus  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Stimulus Indicating Damage to Its DNA From Environmental Insults or Errors During Metabolism. 
    16567   Protein Ubiquitination  The Process in Which One or More Ubiquitin Groups Are Added to a Protein. 
    16574   Histone Ubiquitination  The Modification of Histones by Addition of Ubiquitin Groups. 
    19221   Cytokine Mediated Signaling Pathway  A Series of Molecular Signals Initiated by the Binding of a Cytokine to a Receptor On the Surface of a Cell and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. 
    31058   Positive Regulation of Histone Modification  Any Process That Activates or Increases the Frequency Rate or Extent of the Covalent Alteration of a Histone. 
    33182   Regulation of Histone Ubiquitination  Any Process That Modulates the Frequency Rate or Extent of the Addition of a Ubiquitin Group to a Histone Protein. 
    34134   Toll Like Receptor 2 Signaling Pathway  Any Series of Molecular Signals Generated As a Consequence of Binding to Toll Like Receptor 2. 
    34142   Toll Like Receptor 4 Signaling Pathway  Any Series of Molecular Signals Generated As a Consequence of Binding to Toll Like Receptor 4. 
    34146   Toll Like Receptor 5 Signaling Pathway  Any Series of Molecular Signals Generated As a Consequence of Binding to Toll Like Receptor 5. 
    34162   Toll Like Receptor 9 Signaling Pathway  Any Series of Molecular Signals Generated As a Consequence of Binding to Toll Like Receptor 9. 
    34166   Toll Like Receptor 10 Signaling Pathway  Any Series of Molecular Signals Generated As a Consequence of Binding to Toll Like Receptor 10. 
    35872   Nucleotide Binding Domain Leucine Rich Repeat Containing Receptor Signaling Pathway  A Series of Molecular Signals Generated As a Consequence of a Nucleotide Binding Domain Leucine Rich Repeat Containing Receptor (nlr) Binding to One of Its Physiological Ligands. Nlrs Are Cytoplasmic Receptors Defined by Their Tripartite Domain Architecture That Contains: a Variable C Terminus a Middle Nucleotide Binding Domain and a Lrr Domain That Is Variable in the Repeats Composition and Number. the Nlr Signaling Pathway Begins with Binding of a Ligand to a Nlr Receptor and Ends with Regulation of a Downstream Cellular Process. 
    38095   Fc Epsilon Receptor Signaling Pathway  A Series of Molecular Signals Initiated by the Binding of the Fc Portion of Immunoglobulin E (ige) to an Fc Epsilon Receptor On the Surface of a Signal Receiving Cell and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. the Fc Portion of an Immunoglobulin Is Its C Terminal Constant Region. 
    38123   Toll Like Receptor Tlr1:tlr2 Signaling Pathway  A Series of Molecular Signals Initiated by the Binding of a Heterodimeric Tlr1:tlr2 Complex to One of It's Physiological Ligands Followed by Transmission of the Signal by the Activated Receptor and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. 
    38124   Toll Like Receptor Tlr6:tlr2 Signaling Pathway  A Series of Molecular Signals Initiated by the Binding of a Heterodimeric Tlr6:tlr2 Complex to One of It's Physiological Ligands Followed by Transmission of the Signal by the Activated Receptor and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. 
    43123   Positive Regulation of I Kappab Kinase/nf Kappab Signaling  Any Process That Activates or Increases the Frequency Rate or Extent of I Kappab Kinase/nf Kappab Signaling. 
    45087   Innate Immune Response  Innate Immune Responses Are Defense Responses Mediated by Germline Encoded Components That Directly Recognize Components of Potential Pathogens. 
    45739   Positive Regulation of DNA Repair  Any Process That Activates or Increases the Frequency Rate or Extent of DNA Repair. 
    50852   T Cell Receptor Signaling Pathway  A Series of Molecular Signals Initiated by the Cross Linking of an Antigen Receptor On a T Cell. 
    51092   Positive Regulation of Nf Kappab Transcription Factor Activity  Any Process That Activates or Increases the Frequency Rate or Extent of Activity of the Transcription Factor Nf Kappab. 
    51443   Positive Regulation of Ubiquitin Protein Transferase Activity  Any Process That Activates Maintains or Increases the Rate of Ubiquitin Transferase Activity. 
    70423   Nucleotide Binding Oligomerization Domain Containing Signaling Pathway  Any Series of Molecular Signals Generated As a Consequence of Binding to a Nucleotide Binding Oligomerization Domain Containing (nod) Protein. 
    70534   Protein K63 Linked Ubiquitination  A Protein Ubiquitination Process in Which a Polymer of Ubiquitin Formed by Linkages Between Lysine Residues At Position 63 of the Ubiquitin Monomers Is Added to a Protein. K63 Linked Ubiquitination Does Not Target the Substrate Protein For Degradation But Is Involved in Several Pathways Notably As a Signal to Promote Error Free DNA Postreplication Repair. 
    151   Ubiquitin Ligase Complex  A Protein Complex That Includes a Ubiquitin Protein Ligase and Other Proteins That May Confer Substrate Specificity On the Complex. 
    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. 
    31372   Ubc13 Mms2 Complex  A Heterodimeric Ubiquitin Conjugating Enzyme Complex That Catalyzes Assembly of K63 Linked Polyubiquitin Chains Which Act As a Signal to Promote Error Free DNA Postreplication Repair; in Saccharomyces the Complex Comprises Ubc13p and Mms2p. 
    35370   Ubc13 Uev1a Complex  A Heterodimeric Ubiquitin Conjugating Enzyme Complex That Catalyzes Assembly of K63 Linked Polyubiquitin Chains and Is Involved in Nf Kappab Activation. in Humans At Least the Complex Comprises the Ubiquitin Conjugating Enzyme Ubc13 and Ubiquitin Conjugating Enzyme Variant 1a (uev1a). 
    43234   Protein Complex  Any Macromolecular Complex Composed (only) of Two or More Polypeptide Subunits Along with Any Covalently Attached Molecules (such As Lipid Anchors or Oligosaccharide) or Non Protein Prosthetic Groups (such As Nucleotides or Metal Ions). Prosthetic Group in This Context Refers to a Tightly Bound Cofactor. the Component Polypeptide Subunits May Be Identical. 
    70062   Extracellular Vesicular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. 
    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. 
    16881   Acid Amino Acid Ligase Activity  Catalysis of the Ligation of an Acid to an Amino Acid Via a Carbon Nitrogen Bond with the Concomitant Hydrolysis of the Diphosphate Bond in ATP or a Similar Triphosphate. 
    43130   Ubiquitin Binding  Interacting Selectively and Non Covalently with Ubiquitin a Protein That When Covalently Bound to Other Cellular Proteins Marks Them For Proteolytic Degradation. 
    44822   Poly(a) RNA Binding  Interacting Non Covalently with a Poly(a) RNA a RNA Molecule Which Has a Tail of Adenine Bases. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene ube2n, blu
    Host Scientific Name Escherichia coli  


    Chain A
    Scientific Name Shigella flexneri  
    Gene orf169b, cp0209
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    12 12q22 7334     ubiquitin-conjugating enzyme E2N UBE2N