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Crystal structures of bacterial RNA Polymerase paused elongation complexes
Biology and Chemistry Report
4GZZ
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSCRIPTION/DNA-RNA HYBRID
    Text RNA Polymerase, transcription, paused transcription elongation complex, transcriptional pausing, DNA directed RNA transcription', TRANSCRIPTION-DNA-RNA HYBRID complex

    Polymeric Molecules

    Chain A,B
    Description DNA-directed RNA polymerase subunit alpha 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 35056.5 
    Source Method genetically manipulated  
    Entity Name RNAP subunit alpha, RNA polymerase subunit alpha, Transcriptase subunit alpha 
    Chain C
    Description DNA-directed RNA polymerase subunit beta 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 125437.0 
    Source Method genetically manipulated  
    Entity Name RNAP subunit beta, RNA polymerase subunit beta, Transcriptase subunit beta 
    Chain D
    Description DNA-directed RNA polymerase subunit beta' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 172380.0 
    Source Method genetically manipulated  
    Entity Name RNAP subunit beta', RNA polymerase subunit beta', Transcriptase subunit beta' 
    Chain E
    Description DNA-directed RNA polymerase subunit omega 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 11533.4 
    Source Method genetically manipulated  
    Entity Name RNAP omega subunit, RNA polymerase omega subunit, Transcriptase subunit omega 
    Chain N
    Description non-template DNA 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 4000.7 
    Source Method synthetic  
    Chain R
    Description RNA transcript 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polyribonucleotide 
    Formula Weight 5131.1 
    Source Method synthetic  
    Chain T
    Description template DNA 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 6696.4 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    MG  MAGNESIUM ION  Mg   24.31  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B RPOA_THET8 Q5SHR6     
    C RPOB_THET8 Q5SHB7     
    D RPOC_THET8 Q5SHB8     
    E RPOZ_THET8 Q5SI19     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  2.7.7.6      
    2.7.7.6      
    2.7.7.6      
    2.7.7.6      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    6351   Transcription DNA Templated  The Cellular Synthesis of RNA On a Template of Dna. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    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'. 
    16740   Transferase Activity  Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 
    16779   Nucleotidyltransferase Activity  Catalysis of the Transfer of a Nucleotidyl Group to a Reactant. 
    46983   Protein Dimerization Activity  The Formation of a Protein Dimer a Macromolecular Structure Consists of Two Noncovalently Associated Identical or Nonidentical Subunits. 
    Chain C
    GO ID   Ontology GO Term Definition
    6351   Transcription DNA Templated  The Cellular Synthesis of RNA On a Template of Dna. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    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'. 
    16740   Transferase Activity  Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 
    16779   Nucleotidyltransferase Activity  Catalysis of the Transfer of a Nucleotidyl Group to a Reactant. 
    32549   Ribonucleoside Binding  Interacting Selectively and Non Covalently with a Ribonucleoside a Compound Consisting of a Purine or Pyrimidine Nitrogenous Base Linked to Ribose. 
    Chain D
    GO ID   Ontology GO Term Definition
    6351   Transcription DNA Templated  The Cellular Synthesis of RNA On a Template of Dna. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    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'. 
    16740   Transferase Activity  Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 
    16779   Nucleotidyltransferase Activity  Catalysis of the Transfer of a Nucleotidyl Group to a Reactant. 
    Chain E
    GO ID   Ontology GO Term Definition
    6351   Transcription DNA Templated  The Cellular Synthesis of RNA On a Template of Dna. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    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'. 
    16740   Transferase Activity  Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 
    16779   Nucleotidyltransferase Activity  Catalysis of the Transfer of a Nucleotidyl Group to a Reactant. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain E
    Scientific Name Thermus thermophilus  
    Strain HB8
    Gene rpoz, ttha1561
    Host Scientific Name Thermus thermophilus  
    Host Strain Hb8


    Chain D
    Scientific Name Thermus thermophilus  
    Strain HB8
    Details Genomic Copy of Rpoc Replaced by a C Terminal 10his Tagged Version
    Gene rpoc, ttha1812
    Host Scientific Name Thermus thermophilus  
    Host Strain Hb8


    Chain C
    Scientific Name Thermus thermophilus  
    Strain HB8
    Gene rpob, ttha1813
    Host Scientific Name Thermus thermophilus  
    Host Strain Hb8


    Chain A,B
    Scientific Name Thermus thermophilus  
    Strain HB8
    Gene rpoa, ttha1664
    Host Scientific Name Thermus thermophilus  
    Host Strain Hb8


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    - - 3169128     DNA-directed RNA polymerase subunit alpha TTHA1664    
    - - 3169736     DNA-directed RNA polymerase subunit beta RPOB    
    - - 3169754     DNA-directed RNA polymerase subunit beta' RpoC TTHA1812    
    - - 3169896     DNA-directed RNA polymerase subunit omega RPOZ