Summary: Bacterial RNA polymerase, alpha chain C terminal domain
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Bacterial RNA polymerase, alpha chain C terminal domain Provide feedback
The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal [2].
Literature references
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Jeon YH, Negishi T, Shirakawa M, Yamazaki T, Fujita N, Ishihama A, Kyogoku Y; , Science 1995;270:1495-1497.: Solution structure of the activator contact domain of the RNA polymerase alpha subunit. PUBMED:7491496 EPMC:7491496
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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: | HHH HHH_2 HHH_5 |
Similarity to PfamA using HHSearch: | HHH_5 |
External database links
SCOP: | 1coo |
This tab holds annotation information from the InterPro database.
InterPro entry IPR011260
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. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation [PUBMED:12202833].
The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [PUBMED:7491496].
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) |
DNA binding (GO:0003677) | |
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 HHH (CL0198), which has the following description:
This superfamily includes Helix-hairpin-helix DNA-binding domains.
The clan contains the following 23 members:
Cdd1 DNA_pol_B_N DNA_pol_lambd_f DUF3173 DUF3701 DUF4332 DUF655 HHH HhH-GPD HHH_2 HHH_3 HHH_4 HHH_5 HHH_6 HHH_7 HHH_8 HHH_9 IMS_HHH PsbU RNA_pol_A_CTD T2SSK TfoX_C Transposase_20Alignments
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 (63) |
Full (8478) |
Representative proteomes | UniProt (29047) |
NCBI (23841) |
Meta (2144) |
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RP15 (2405) |
RP35 (5992) |
RP55 (8737) |
RP75 (12271) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (63) |
Full (8478) |
Representative proteomes | UniProt (29047) |
NCBI (23841) |
Meta (2144) |
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RP15 (2405) |
RP35 (5992) |
RP55 (8737) |
RP75 (12271) |
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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: | 63 |
Number in full: | 8478 |
Average length of the domain: | 65.90 aa |
Average identity of full alignment: | 43 % |
Average coverage of the sequence by the domain: | 19.93 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 67 | ||||||||||||
Family (HMM) version: | 15 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 9 interactions for this family. More...
ArsC RNA_pol_L RNA_pol_Rpb1_2 HHH_5 RNA_pol_A_CTD RNA_pol_Rpb2_6 RNA_pol_Rpb6 Sigma70_r4 HTH_18Structures
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_CTD domain has been found. There are 60 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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