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APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP
Biology and Chemistry Report
1R4N
  •   Structure Details   Hide

    Structure Keywords

    Keywords CELL CYCLE
    Text CELL CYCLE

    Polymeric Molecules

    Chain A,C,E,G
    Description amyloid beta precursor protein-binding protein 1 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 59830.3 
    Source Method genetically manipulated  
    Entity Name APPBP1 
    Chain B,D,F,H
    Description ubiquitin-activating enzyme E1C 
    Mutation C216A 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 48394.7 
    Source Method genetically manipulated  
    Entity Name UBA3 
    Chain I,J,K,L
    Description Ubiquitin-like protein NEDD8 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 8574.1 
    Source Method genetically manipulated  
    Entity Name NEDD8 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ATP  ADENOSINE-5'-TRIPHOSPHATE  C10 H16 N5 O13 P3   507.18  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,C,E,G ULA1_HUMAN A6NCK0     
    B,D,F,H UBA3_HUMAN A6NLB5     
    I,J,K,L NEDD8_HUMAN Q15843     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    B D F H  6.3.2      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,C,E,G
    GO ID   Ontology GO Term Definition
    6915   Apoptotic Process  A Programmed Cell Death Process Which Begins When a Cell Receives an Internal (e.g. DNA Damage) or External Signal (e.g. an Extracellular Death Ligand) and Proceeds Through a Series of Biochemical Events (signaling Pathway Phase) Which Trigger an Execution Phase. the Execution Phase Is the Last Step of an Apoptotic Process and Is Typically Characterized by Rounding Up of the Cell Retraction of Pseudopodes Reduction of Cellular Volume (pyknosis) Chromatin Condensation Nuclear Fragmentation (karyorrhexis) Plasma Membrane Blebbing and Fragmentation of the Cell Into Apoptotic Bodies. When the Execution Phase Is Completed the Cell Has Died. 
    7049   Cell Cycle  The Progression of Biochemical and Morphological Phases and Events That Occur in a Cell During Successive Cell Replication or Nuclear Replication Events. Canonically the Cell Cycle Comprises the Replication and Segregation of Genetic Material Followed by the Division of the Cell But in Endocycles or Syncytial Cells Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division. 
    7165   Signal Transduction  The Cellular Process in Which a Signal Is Conveyed to Trigger a Change in the Activity or State of a Cell. Signal Transduction Begins with Reception of a Signal (e.g. a Ligand Binding to a Receptor or Receptor Activation by a Stimulus Such As Light) or For Signal Transduction in the Absence of Ligand Signal Withdrawal or the Activity of a Constitutively Active Receptor. Signal Transduction Ends with Regulation of a Downstream Cellular Process E.g. Regulation of Transcription or Regulation of a Metabolic Process. Signal Transduction Covers Signaling From Receptors Located On the Surface of the Cell and Signaling Via Molecules Located Within the Cell. For Signaling Between Cells Signal Transduction Is Restricted to Events At and Within the Receiving Cell. 
    33314   Mitotic DNA Replication Checkpoint  A Cell Cycle Checkpoint That Acts During a Mitotic Cell Cycle and Prevents the Initiation of Mitosis Until DNA Replication Is Complete Thereby Ensuring That Progeny Inherit a Full Complement of the Genome. 
    42981   Regulation of Apoptotic Process  Any Process That Modulates the Occurrence or Rate of Cell Death by Apoptotic Process. 
    43523   Regulation of Neuron Apoptotic Process  Any Process That Modulates the Occurrence or Rate of Cell Death by Apoptotic Process in Neurons. 
    45116   Protein Neddylation  Covalent Attachment of the Ubiquitin Like Protein Nedd8 (rub1) to Another Protein. 
    51402   Neuron Apoptotic Process  Any Apoptotic Process in a Neuron the Basic Cellular Unit of Nervous Tissue. Each Neuron Consists of a Body an Axon and Dendrites. Their Purpose Is to Receive Conduct and Transmit Impulses in the Nervous System. 
    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. 
    5886   Plasma Membrane  The Membrane Surrounding a Cell That Separates the Cell From Its External Environment. It Consists of a Phospholipid Bilayer and Associated Proteins. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    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. 
    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). 
    19781   Nedd8 Activating Enzyme Activity  Catalysis of the Initiation of the Nedd8 (rub1) Conjugation Cascade. 
    31625   Ubiquitin Protein Ligase Binding  Interacting Selectively and Non Covalently with a Ubiquitin Protein Ligase Enzyme Any of the E3 Proteins. 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 
    Chain B,D,F,H
    GO ID   Ontology GO Term Definition
    278   Mitotic Cell Cycle  Progression Through the Phases of the Mitotic Cell Cycle the Most Common Eukaryotic Cell Cycle Which Canonically Comprises Four Successive Phases Called G1 S G2 and M and Includes Replication of the Genome and the Subsequent Segregation of Chromosomes Into Daughter Cells. in Some Variant Cell Cycles Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division or G1 and G2 Phases May Be Absent. 
    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. 
    7049   Cell Cycle  The Progression of Biochemical and Morphological Phases and Events That Occur in a Cell During Successive Cell Replication or Nuclear Replication Events. Canonically the Cell Cycle Comprises the Replication and Segregation of Genetic Material Followed by the Division of the Cell But in Endocycles or Syncytial Cells Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division. 
    7113   Endomitotic Cell Cycle  A Mitotic Cell Cycle in Which Chromosomes Are Replicated and Sister Chromatids Separate But Spindle Formation Nuclear Membrane Breakdown and Nuclear Division Do Not Occur Resulting in an Increased Number of Chromosomes in the Cell. 
    45116   Protein Neddylation  Covalent Attachment of the Ubiquitin Like Protein Nedd8 (rub1) to Another Protein. 
    51726   Regulation of Cell Cycle  Any Process That Modulates the Rate or Extent of Progression Through the Cell Cycle. 
    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. 
    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. 
    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. 
    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. 
    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. 
    19781   Nedd8 Activating Enzyme Activity  Catalysis of the Initiation of the Nedd8 (rub1) Conjugation Cascade. 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 
    Chain I,J,K,L
    GO ID   Ontology GO Term Definition
    6357   Regulation of Transcription From RNA Polymerase Ii Promoter  Any Process That Modulates the Frequency Rate or Extent of Transcription From an RNA Polymerase Ii Promoter. 
    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. 
    7179   Transforming Growth Factor Beta Receptor Signaling Pathway  A Series of Molecular Signals Initiated by the Binding of an Extracellular Ligand to a Transforming Growth Factor Beta Receptor On the Surface of a Target Cell and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. 
    8104   Protein Localization  Any Process in Which a Protein Is Transported to or Maintained in a Specific Location. 
    9653   Anatomical Structure Morphogenesis  The Process in Which Anatomical Structures Are Generated and Organized. Morphogenesis Pertains to the Creation of Form. 
    14070   Response to Organic Cyclic Compound  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of an Organic Cyclic Compound Stimulus. 
    45116   Protein Neddylation  Covalent Attachment of the Ubiquitin Like Protein Nedd8 (rub1) to Another 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. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    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. 
    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). 
    31625   Ubiquitin Protein Ligase Binding  Interacting Selectively and Non Covalently with a Ubiquitin Protein Ligase Enzyme Any of the E3 Proteins. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain I,J,K,L
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene nedd8
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia


    Chain B,D,F,H
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia


    Chain A,C,E,G
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    3 3p14.1 9039     ubiquitin-like modifier activating enzyme 3 UBA3    
    14 14q12 4738     neural precursor cell expressed, developmentally down-regulated 8 NEDD8    
    16 16q22 8883     NEDD8 activating enzyme E1 subunit 1 NAE1    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs11556607 LS-SNP   dbSNP   A 32 H - > Y Coil 23% (Intermediate) 16 66860643
    rs199964855 LS-SNP   dbSNP   A 43 T - > N Helix 0% (Buried) 16 66860609
    rs137985751 LS-SNP   dbSNP   A 56 S - > L Beta Ladder 17% (Intermediate) 16 66860477
    rs77699528 LS-SNP   dbSNP   A 73 N - > I Coil 3% (Buried) 16 66860426
    rs200163314 LS-SNP   dbSNP   A 90 M - > V Helix 12% (Intermediate) 16 66857485
    rs363212 LS-SNP   dbSNP   A 101 S - > F Beta Ladder 48% (Exposed) 16 66857451
    rs140382369 LS-SNP   dbSNP   A 115 N - > S Helix 82% (Exposed) 16 66857187
    rs111458825 LS-SNP   dbSNP   A 155 T - > A Beta Ladder 1% (Buried) 16 66855401
    rs143652293 LS-SNP   dbSNP   A 165 I - > V Beta Ladder 2% (Buried) 16 66855371
    rs201659718 LS-SNP   dbSNP   A 237 Y - > D Turn 55% (Exposed) 16 66850907
    rs149417383 LS-SNP   dbSNP   A 237 Y - > C Turn 55% (Exposed) 16 66850906
    rs201813040 LS-SNP   dbSNP   A 262 E - > K Coil 6% (Buried) 16 66850540
    rs200655956 LS-SNP   dbSNP   A 269 I - > M Helix 2% (Buried) 16 66850517
    rs35391524 LS-SNP   dbSNP   A 309 R - > H Helix 19% (Intermediate) 16 66847575
    rs186580935 LS-SNP   dbSNP   A 356 A - > T Helix 14% (Intermediate) 16 66844644
    rs187763841 LS-SNP   dbSNP   A 450 V - > I Helix 23% (Intermediate) 16 66839912
    rs141920415 LS-SNP   dbSNP   A 468 Y - > C Turn 9% (Buried) 16 66839857
    rs11556608 LS-SNP   dbSNP   A 480 H - > N Helix 43% (Exposed) 16 66839822
    rs150893619 LS-SNP   dbSNP   A 509 I - > V Helix 11% (Intermediate) 16 66836992
    rs141151787 LS-SNP   dbSNP   A 510 T - > S Helix 9% (Intermediate) 16 66836988
    rs139734072 LS-SNP   dbSNP   B 44 F - > L Helix 61% (Exposed) 3 69124650
    rs186063144 LS-SNP   dbSNP   B 47 D - > G Helix 49% (Exposed) 3 69124642
    rs142785164 LS-SNP   dbSNP   B 48 T - > I Helix 45% (Exposed) 3 69124639
    rs71302167 LS-SNP   dbSNP   B 60 G - > R Helix 0% (Buried) 3 69124604
    rs188636684 LS-SNP   dbSNP   B 116 P - > L Turn 38% (Exposed) 3 69117097
    rs11544139 LS-SNP   dbSNP   B 122 P - > Q Beta Ladder 18% (Intermediate) 3 69117079
    rs199541209 LS-SNP   dbSNP   B 159 I - > V Helix 15% (Intermediate) 3 69112288
    rs149049620 LS-SNP   dbSNP   B 182 T - > A Beta Ladder 1% (Buried) 3 69112219
    rs144568523 LS-SNP   dbSNP   B 196 M - > K Turn 62% (Exposed) 3 69112176
    rs150571999 LS-SNP   dbSNP   B 203 T - > M 3/10 Helix 3% (Buried) 3 69112155
    rs150359494 LS-SNP   dbSNP   B 221 M - > K Coil 9% (Buried) 3 69111299
    rs11544137 LS-SNP   dbSNP   B 234 M - > V Helix 37% (Exposed) 3 69111261
    rs141743890 LS-SNP   dbSNP   B 239 K - > Q Helix 57% (Exposed) 3 69111246
    rs116820810 LS-SNP   dbSNP   B 245 E - > G Bend 89% (Exposed) 3 69111078
    rs201471678 LS-SNP   dbSNP   B 277 T - > M Coil 53% (Exposed) 3 69110982
    rs140550798 LS-SNP   dbSNP   B 360 K - > I Coil 33% (Intermediate) 3 69105376
    rs74744808 LS-SNP   dbSNP   I 138 P - > Q 3/10 Helix 24% (Intermediate) 14 24687375
    rs113779918 LS-SNP   dbSNP   I 148 K - > E Beta Ladder 50% (Exposed) 14 24687346