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Thermus thermophilus RNA polymerase de novo transcription initiation complex
Biology and Chemistry Report
4Q4Z
  •   Structure Details   Hide

    Structure Keywords

    Keywords transcription/DNA
    Text transcription, DNA and NTP, transcription-DNA 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 natural source  
    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 natural source  
    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 170999.0 
    Source Method natural source  
    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 natural source  
    Entity Name RNAP omega subunit, RNA polymerase omega subunit, Transcriptase subunit omega 
    Chain F
    Description RNA polymerase sigma factor SigA 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 48598.6 
    Source Method genetically manipulated  
    Chain G
    Description DNA (5'-D(*CP*CP*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*GP*CP*AP*GP*CP*CP*A)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 6713.4 
    Source Method synthetic  
    Chain H
    Description DNA (25-MER) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 8421.5 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    2TM  5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine  C10 H18 N3 O13 P3   481.18  View 
    ATP  ADENOSINE-5'-TRIPHOSPHATE  C10 H16 N5 O13 P3   507.18  View 
    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_THETH Q9Z9H6     
    C RPOB_THET8 Q5SHB7     
    D RPOC_THET8 Q5SHB8     
    F Q5SKW1_THET8 Q5SKW1     

    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. 
    Chain F
    GO ID   Ontology GO Term Definition
    1123   Transcription Initiation From Bacterial Type RNA Polymerase Promoter  Any Process Involved in the Assembly of Bacterial Type RNA Polymerase Preinitiation Complex (pic) At the Core 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. the Initiation Phase Ends Just Before and Does Not Include Promoter Clearance or Release Which Is the Transition Between the Initiation and Elongation Phases of Transcription. 
    6351   Transcription DNA Templated  The Cellular Synthesis of RNA On a Template of Dna. 
    6352   DNA Templated Transcription Initiation  Any Process Involved in the Assembly of the RNA Polymerase Preinitiation Complex (pic) At the Core 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. the Initiation Phase Ends Just Before and Does Not Include Promoter Clearance or Release Which Is the Transition Between the Initiation and Elongation Phases of Transcription. 
    6355   Regulation of Transcription DNA Templated  Any Process That Modulates the Frequency Rate or Extent of Cellular DNA Templated Transcription. 
    10468   Regulation of Gene Expression  Any Process That Modulates the Frequency Rate or Extent of Gene Expression. Gene Expression Is the Process in Which a Gene's Coding Sequence Is Converted Into a Mature Gene Product or Products (proteins or Rna). This Includes the Production of an RNA Transcript As Well As Any Processing to Produce a Mature RNA Product or an MRNA (for Protein Coding Genes) and the Translation of That MRNA Into Protein. Some Protein Processing Events May Be Included When They Are Required to Form an Active Form of a Product From an Inactive Precursor Form. 
    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). 
    3700   Sequence Specific DNA Binding Transcription Factor Activity  Interacting Selectively and Non Covalently with a Specific DNA Sequence in Order to Modulate Transcription. the Transcription Factor May or May Not Also Interact Selectively with a Protein or Macromolecular Complex. 
    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. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Natural Source

    Chain E
    Scientific Name Thermus thermophilus  
    Strain HB8
    Chain D
    Scientific Name Thermus thermophilus  
    Strain HB8
    Chain C
    Scientific Name Thermus thermophilus  
    Strain HB8
    Chain A,B
    Scientific Name Thermus thermophilus  
    Strain HB8

    Genetic Source

    Chain F
    Scientific Name Thermus thermophilus  
    Strain HB8
    Gene siga, ttha0532
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Pet
    Host Plasmid Name pET21a-SigA


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    - - 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    
    - - 3169450     RNA polymerase pricipal sigma factor RpoD TTHA0532