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Crystal structure of the RNA polymerase holoenzyme from Thermus thermophilus at 2.6A resolution
Biology and Chemistry Report
1IW7
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE
    Text RNA polymerase holoenzyme, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, TRANSFERASE

    Polymeric Molecules

    Chain A,B,K,L
    Description RNA polymerase alpha subunit 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 35056.5 
    Source Method natural source  
    Chain C,M
    Description RNA polymerase beta subunit 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 125437.0 
    Source Method natural source  
    Chain D,N
    Description RNA polymerase beta subunit 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 170999.0 
    Source Method natural source  
    Chain E,O
    Description RNA polymerase omega subunit 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 11521.3 
    Source Method natural source  
    Chain F,P
    Description RNA polymerase sigma-70 subunit 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 48568.6 
    Source Method natural source  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    MG  MAGNESIUM ION  Mg   24.31  View 
    PB  LEAD (II) ION  Pb   207.20  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,K,L RPOA_THETH Q9Z9H6     
    C,M RPOB_THET8 Q5SHB7     
    D,N RPOC_THET8 Q5SHB8     
    E,O RPOZ_THET8 Q5SI19     
    F,P SIGA_THET2 Q72L95     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B K L  2.7.7.6      
    C M  2.7.7.6      
    D N  2.7.7.6      
    E O  2.7.7.6      
    F P  2.7.7.6      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,K,L
    GO ID   Ontology GO Term Definition
    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 C,M
    GO ID   Ontology GO Term Definition
    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 D,N
    GO ID   Ontology GO Term Definition
    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,O
    GO ID   Ontology GO Term Definition
    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 F,P
    GO ID   Ontology GO Term Definition
    6351   Transcription DNA Templated  The Cellular Synthesis of RNA On a Template of Dna. 
    6355   Regulation of Transcription DNA Templated  Any Process That Modulates the Frequency Rate or Extent of Cellular DNA Templated Transcription. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    16987   Sigma Factor Activity  A Sigma Factor Is the Promoter Specificity Subunit of Eubacterial Type Multisubunit RNA Polymerases Those Whose Core Subunit Composition Is Often Described As Alpha(2) Beta Beta Prime. (this Type of Multisubunit RNA Polymerase Complex Is Known to Be Found in Eubacteria and Plant Plastids). Although Sigma Does Not Bind DNA On Its Own When Combined with the Core to Form the Holoenzyme This Binds Specifically to Promoter Sequences with the Sigma Factor Making Sequence Specific Contacts with the Promoter Elements. the Sigma Subunit Is Released From the Elongating Form of the Polymerase and Is Thus Free to Act Catalytically For Multiple RNA Polymerase Core Enzymes. 


     
  •   Gene Details   Hide

    Natural Source

    Chain F,P
    Scientific Name Thermus thermophilus  
    Genus Thermus
    Chain E,O
    Scientific Name Thermus thermophilus  
    Genus Thermus
    Chain D,N
    Scientific Name Thermus thermophilus  
    Genus Thermus
    Chain C,M
    Scientific Name Thermus thermophilus  
    Genus Thermus
    Chain A,B,K,L
    Scientific Name Thermus thermophilus  
    Genus Thermus