Summary: RNA polymerase Rpb2, domain 6
RNA polymerase Rpb2, domain 6 Provide feedback
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 . 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 . This domain is also involved in binding to Rpb1 and Rpb3 . Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
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This tab holds annotation information from the InterPro database.
InterPro entry IPR007120
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 polymerases (EC) 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 [PUBMED:11313498]. 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 [PUBMED:11313498]. This domain is also involved in binding to Rpb1 and Rpb3 [PUBMED:11313498]. Many of the bacterial members contain large insertions within this domain, which are known as dispensable region 2 (DRII).
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)|
|DNA binding (GO:0003677)|
|Biological process||transcription, DNA-templated (GO:0006351)|
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Late expression factor 8 (LEF-8) is one of the primary components of RNA polymerase produced by polyhedrosis viruses. LEF-8 shows homology to domain 6 of the second largest subunit of prokaryotic DNA-directed RNA polymerase.
The clan contains the following 2 members:LEF-8 RNA_pol_Rpb2_6
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Number in seed:||74|
|Number in full:||36331|
|Average length of the domain:||356.10 aa|
|Average identity of full alignment:||44 %|
|Average coverage of the sequence by the domain:||40.11 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||24|
|Download:||download the raw HMM for this family|
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There are 32 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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_Rpb2_6 domain has been found. There are 215 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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