Summary: RNA polymerase Rpb2, domain 2
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RNA polymerase Rpb2, domain 2 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). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain . DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble . Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
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This tab holds annotation information from the InterPro database.
InterPro entry IPR007642
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). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [PUBMED:11313498]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, a region known as dispensable region 1 (DRI).
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|Molecular function||DNA-directed RNA polymerase activity (GO:0003899)|
|DNA binding (GO:0003677)|
|Biological process||transcription, DNA-dependent (GO:0006351)|
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Curation and family details
|Number in seed:||22|
|Number in full:||13001|
|Average length of the domain:||126.70 aa|
|Average identity of full alignment:||21 %|
|Average coverage of the sequence by the domain:||18.82 %|
|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:||9|
|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_Rpb2_2 domain has been found. There are 145 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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