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190  structures 6156  species 9  interactions 7433  sequences 28  architectures

Family: RNA_pol_L (PF01193)

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

  1. 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

  2. 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

  3. 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

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011261

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.
Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.

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 subunit (RpoA) 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]. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [PUBMED:9657722].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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_2

Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(218)
Full
(7433)
Representative proteomes NCBI
(5625)
Meta
(2992)
RP15
(593)
RP35
(1066)
RP55
(1406)
RP75
(1663)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(218)
Full
(7433)
Representative proteomes NCBI
(5625)
Meta
(2992)
RP15
(593)
RP35
(1066)
RP55
(1406)
RP75
(1663)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(218)
Full
(7433)
Representative proteomes NCBI
(5625)
Meta
(2992)
RP15
(593)
RP35
(1066)
RP55
(1406)
RP75
(1663)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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 View help on the curation process

Seed source: Pfam-B_172 (release 3.0)
Previous IDs: none
Type: Domain
Author: Finn RD
Number in seed: 218
Number in full: 7433
Average length of the domain: 199.80 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 64.81 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 18.9 18.9
Trusted cut-off 18.9 18.9
Noise cut-off 18.8 18.8
Model length: 66
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 9 interactions for this family. More...

RNA_pol_A_bac DNA_RNApol_7kD RNA_pol_N RNA_pol_Rpb1_2 RNA_pol_L RNA_pol_Rpb1_4 RNA_pol_Rpb1_3 RNA_pol_Rpb8 RNA_pol_Rpb2_6

Structures

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 190 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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