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Crystal structure of yeast subcomplex of Rpb4 and Rpb7
Biology and Chemistry Report
1Y14
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE
    Text transferase

    Polymeric Molecules

    Chain A,C
    Description DNA-directed RNA polymerase II 32 kDa polypeptide 
    Fragment residues 35-221 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 21436.9 
    Source Method genetically manipulated  
    Entity Name B32, Rpb4 
    Chain B,D
    Description DNA-directed RNA polymerase II 19 kDa polypeptide 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 19081.2 
    Source Method genetically manipulated  
    Entity Name B16, Rpb7 

     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,C RPB4_YEAST D6VW44     
    B,D RPB7_YEAST D6VT36     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A C  2.7.7.6      
    B D  2.7.7.6      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,C
    GO ID   Ontology GO Term Definition
    6351   Transcription DNA Templated  The Cellular Synthesis of RNA On a Template of Dna. 
    44237   Cellular Metabolic Process  The Chemical Reactions and Pathways by Which Individual Cells Transform Chemical Substances. 
    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. 
    3899   DNA Directed RNA Polymerase Activity  Catalysis of the Reaction: Nucleoside Triphosphate + Rna(n) = Diphosphate + Rna(n+1). Utilizes a DNA Template I.e. the Catalysis of DNA Template Directed Extension of the 3' End of an RNA Strand by One Nucleotide At a Time. Can Initiate a Chain 'de Novo'. 
    Chain B,D
    GO ID   Ontology GO Term Definition
    291   Nuclear Transcribed MRNA Catabolic Process Exonucleolytic  The Chemical Reactions and Pathways Resulting in the Breakdown of the Transcript Body of a Nuclear Transcribed MRNA That Occurs When the Ends Are Not Protected by the 5' Cap or the 3' Poly(a) Tail. 
    1172   Transcription RNA Templated  The Cellular Synthesis of RNA On a Template of Rna. 
    6351   Transcription DNA Templated  The Cellular Synthesis of RNA On a Template of Dna. 
    6366   Transcription From RNA Polymerase Ii Promoter  The Synthesis of RNA From a DNA Template by RNA Polymerase Ii Originating At an RNA Polymerase Ii Promoter. Includes Transcription of Messenger RNA (mrna) and Certain Small Nuclear Rnas (snrnas). 
    6367   Transcription Initiation From RNA Polymerase Ii Promoter  Any Process Involved in the Assembly of the RNA Polymerase Ii Preinitiation Complex (pic) At an RNA Polymerase Ii Promoter Region of a DNA Template Resulting in the Subsequent Synthesis of RNA From That Promoter. the Initiation Phase Includes Pic Assembly and the Formation of the First Few Bonds in the RNA Chain Including Abortive Initiation Which Occurs When the First Few Nucleotides Are Repeatedly Synthesized and Then Released. Promoter Clearance or Release Is the Transition Between the Initiation and Elongation Phases of Transcription. 
    45948   Positive Regulation of Translational Initiation  Any Process That Activates or Increases the Frequency Rate or Extent of Translational Initiation. 
    60213   Positive Regulation of Nuclear Transcribed MRNA Poly(a) Tail Shortening  Any Process That Increases the Frequency Rate or Extent of Poly(a) Tail Shortening of a Nuclear Transcribed Mrna. Poly(a) Tail Shortening Is the Decrease in Length of the Poly(a) Tail of an MRNA From Full Length to an Oligo(a) Length. 
    932   Cytoplasmic MRNA Processing Body  A Focus in the Cytoplasm Where Mrnas May Become Inactivated by Decapping or Some Other Mechanism. MRNA Processing and Binding Proteins Are Localized to These Foci. 
    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. 
    5665   DNA Directed RNA Polymerase Ii Core Complex  RNA Polymerase Ii One of Three Nuclear DNA Directed RNA Polymerases Found in All Eukaryotes Is a Multisubunit Complex; Typically It Produces Mrnas Snornas and Some of the Snrnas. Two Large Subunits Comprise the Most Conserved Portion Including the Catalytic Site and Share Similarity with Other Eukaryotic and Bacterial Multisubunit RNA Polymerases. the Largest Subunit of RNA Polymerase Ii Contains an Essential Carboxyl Terminal Domain (ctd) Composed of a Variable Number of Heptapeptide Repeats (ysptsps). the Remainder of the Complex Is Composed of Smaller Subunits (generally Ten or More) Some of Which Are Also Found in RNA Polymerases I and Iii. Although the Core Is Competent to Mediate Ribonucleic Acid Synthesis It Requires Additional Factors to Select the Appropriate Template. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    3697   Single Stranded DNA Binding  Interacting Selectively and Non Covalently with Single Stranded Dna. 
    3723   RNA Binding  Interacting Selectively and Non Covalently with an RNA Molecule or a Portion Thereof. 
    3727   Single Stranded RNA Binding  Interacting Selectively and Non Covalently with Single Stranded Rna. 
    3899   DNA Directed RNA Polymerase Activity  Catalysis of the Reaction: Nucleoside Triphosphate + Rna(n) = Diphosphate + Rna(n+1). Utilizes a DNA Template I.e. the Catalysis of DNA Template Directed Extension of the 3' End of an RNA Strand by One Nucleotide At a Time. Can Initiate a Chain 'de Novo'. 
    3968   RNA Directed RNA Polymerase Activity  Catalysis of the Reaction: Nucleoside Triphosphate + Rna(n) = Diphosphate + Rna(n+1); Uses an RNA Template. 
    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). 
    31369   Translation Initiation Factor Binding  Interacting Selectively and Non Covalently with a Translation Initiation Factor Any Polypeptide Factor Involved in the Initiation of Ribosome Mediated Translation. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B,D
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Genus Saccharomyces
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia


    Chain A,C
    Common Name Baker's Yeast
    Scientific Name Saccharomyces cerevisiae  
    Genus Saccharomyces
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    X - 853301     DNA-directed RNA polymerase II subunit RPB4 RPB4    
    IV - 852013     DNA-directed RNA polymerase II subunit RPB7 RPB7