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Thermus thermophilus RNA polymerase initially transcribing complex containing 6-mer RNA
Annotation data related to this entry.
4Q5S
  •   Protein Family Annotation: Pfam Classification   Hide
    Chain Pfam Accession Pfam Family Identifier Pfam Description Type Comment
    F PF00140   Sigma70_r1_2 Sigma-70 factor, region 1.2 Family
    C PF04563   RNA_pol_Rpb2_1 RNA polymerase beta subunit Family
    D PF00623   RNA_pol_Rpb1_2 RNA polymerase Rpb1, domain 2 Domain RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2]. Source: Pfam  
    A PF01000   RNA_pol_A_bac RNA polymerase Rpb3/RpoA insert domain Domain Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal Source: Pfam  
    D PF05000   RNA_pol_Rpb1_4 RNA polymerase Rpb1, domain 4 Domain RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2]. Source: Pfam  
    C PF00562   RNA_pol_Rpb2_6 RNA polymerase Rpb2, domain 6 Domain RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII). Source: Pfam  
    C PF04565   RNA_pol_Rpb2_3 RNA polymerase Rpb2, domain 3 Domain RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1]. Source: Pfam  
    D PF04997   RNA_pol_Rpb1_1 RNA polymerase Rpb1, domain 1 Domain RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2]. Source: Pfam  
    C PF04560   RNA_pol_Rpb2_7 RNA polymerase Rpb2, domain 7 Domain RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1]. Source: Pfam  
    D PF04998   RNA_pol_Rpb1_5 RNA polymerase Rpb1, domain 5 Domain RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2]. Source: Pfam  
    F PF04539   Sigma70_r3 Sigma-70 region 3 Family
    C PF04561   RNA_pol_Rpb2_2 RNA polymerase Rpb2, domain 2 Domain RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI). Source: Pfam  
    D PF04983   RNA_pol_Rpb1_3 RNA polymerase Rpb1, domain 3 Domain RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2]. Source: Pfam  
    C PF10385   RNA_pol_Rpb2_45 RNA polymerase beta subunit external 1 domain Domain RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region [1]. Source: Pfam  
    E PF01192   RNA_pol_Rpb6 RNA polymerase Rpb6 Family
    D PF04997   RNA_pol_Rpb1_1 RNA polymerase Rpb1, domain 1 Domain RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2]. Source: Pfam  
    A PF01193   RNA_pol_L RNA polymerase Rpb3/Rpb11 dimerisation domain Domain The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Source: Pfam  
    F PF04542   Sigma70_r2 Sigma-70 region 2 Domain Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [1,2]. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation [1,2]. Source: Pfam  
     
  •   Gene Product Annotation: GO Terms   Hide
    Polymer Molecular Function Biological Process Cellular Component
    DNA-directed RNA polymerase subunit alpha (4Q5S:A,B)
    • none
    DNA-directed RNA polymerase subunit beta (4Q5S:C)
    • none
    DNA-directed RNA polymerase subunit beta' (4Q5S:D)
    • none
    DNA-directed RNA polymerase subunit omega (4Q5S:E)
    • none
    RNA polymerase sigma factor SigA (4Q5S:F)
    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') (4Q5S:G)
    • none
    • none
    • none
    DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)- 3') (4Q5S:H)
    • none
    • none
    • none
    RNA (5'-R(P*CP*UP*CP*AP*C)-3') (4Q5S:I)
    • none
    • none
    • none
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Annotations in orange boxes have been gathered from external resources.