Summary: RNA polymerase Rpb3/Rpb11 dimerisation domain
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RNA polymerase Rpb3/Rpb11 dimerisation domain Provide feedback
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 (PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (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.
Literature references
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Zhang G, Darst SA; , Science 1998;281:262-266.: Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain. PUBMED:9657722 EPMC:9657722
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Ebright RH, Busby S; , Curr Opin Genet Dev 1995;5:197-203.: The Escherichia coli RNA polymerase alpha subunit: structure and function. PUBMED:7613089 EPMC:7613089
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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
SCOOP: | Fer4 Fer4_10 Fer4_6 Fer4_7 Fer4_9 RNA_pol_A_bac RNA_pol_L_2 |
Similarity to PfamA using HHSearch: | RNA_pol_A_bac RNA_pol_L_2 |
External database links
HOMSTRAD: | RNA_pol_A_bac |
SCOP: | 1bdf |
This tab holds annotation information from the InterPro database.
InterPro entry IPR011263
The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact, and plays a direct role in promoter recognition [PUBMED:10972792]. In eukaryotes, RNA polymerase (RNAP) II is responsible for all mRNA synthesis. RNAP-II consists of 12 subunits, where subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the bacterial RpoA homodimer [PUBMED:12860379]. Archaeal RNAP closely resembles eukaryotic RNAP-II, and is composed of 12 subunits, of which D and L form a heterodimer resembling the Rpb3/Rpb11 and RpoA/RpoA dimers [PUBMED:12694606].
The bacterial RpoA, eukaryotic Rpb3 and archaeal D subunits share sequence and structural motifs, and can be placed into a single family. These subunits also have unique sequence motifs, especially at their C-terminal ends, which are involved in promoter specificity, for example the CTD of the bacterial RNAP alpha subunit (INTERPRO).
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | DNA-directed 5'-3' RNA polymerase activity (GO:0003899) |
Biological process | transcription, DNA-templated (GO:0006351) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan RBP11-like (CL0509), which has the following description:
This superfamily is characterised by all members carrying RNA Polymerase alpha subunit, chain A, domain 2. The member families form homo- and hetero-dimers.
The clan contains the following 2 members:
RNA_pol_L RNA_pol_L_2Alignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (396) |
Full (9962) |
Representative proteomes | UniProt (47299) |
NCBI (44902) |
Meta (3019) |
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RP15 (1517) |
RP35 (4766) |
RP55 (9208) |
RP75 (15195) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
Seed (396) |
Full (9962) |
Representative proteomes | UniProt (47299) |
NCBI (44902) |
Meta (3019) |
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RP15 (1517) |
RP35 (4766) |
RP55 (9208) |
RP75 (15195) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Pfam-B_172 (release 3.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 396 |
Number in full: | 9962 |
Average length of the domain: | 211.40 aa |
Average identity of full alignment: | 28 % |
Average coverage of the sequence by the domain: | 64.19 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 74 | ||||||||||||
Family (HMM) version: | 25 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 19 interactions for this family. More...
RNA_pol_Rpb6 RNA_pol_N RNA_pol_Rpb1_3 RNA_pol_Rpb1_3 RNA_pol_N RNA_pol_L_2 RNA_pol_L RNA_pol_Rpb2_7 RNA_pol_Rpb1_4 RNA_pol_A_bac RNA_pol_Rpb1_2 RNA_pol_Rpb2_6 RNA_pol_A_bac RNA_pol_Rpb1_1 RNA_pol_Rpb2_6 RNA_pol_Rpb8 RNA_pol_A_CTD RNA_pol_Rpb1_2 RNA_pol_L_2Structures
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_L domain has been found. There are 767 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 sequence.
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