Summary: RNA polymerase Rpb3/RpoA insert domain
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RNA polymerase Rpb3/RpoA insert domain Provide feedback
Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal
Murakami K, Kimura M, Owens JT, Meares CF, Ishihama A; , Proc Natl Acad Sci USA 1997;94:1709-1714.: The two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element. PUBMED:9050843 EPMC:9050843
Internal database links
|Similarity to PfamA using HHSearch:||RNA_pol_L|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR011262
DNA-directed RNA polymerases EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme [PUBMED:3052291]. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [PUBMED:10499798]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.
RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:
- RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.
- RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.
- RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.
RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha (RpoA) subunit homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact [PUBMED:11453250].
The dimerisation domains differ between the different subunit families. In eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (INTERPRO), the dimerisation domain is comprised of a central insert domain, which interrupts an Rpb11-like domain (INTERPRO), dividing it into two halves [PUBMED:9657722]. In eukaryotic Rpb11 and archaeal L subunits, the insert domain is lacking, leaving the Rpb11-like domain intact and contiguous.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||DNA-directed RNA polymerase activity (GO:0003899)|
|protein dimerization activity (GO:0046983)|
|Biological process||transcription, DNA-dependent (GO:0006351)|
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Curation and family details
|Seed source:||Pfam-B_172 (release 3.0)|
|Number in seed:||59|
|Number in full:||7300|
|Average length of the domain:||120.20 aa|
|Average identity of full alignment:||33 %|
|Average coverage of the sequence by the domain:||38.59 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||21|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the RNA_pol_A_bac domain has been found. There are 183 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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