This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme PMID:9670025. In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex PMID:12242451.
This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme [ (PUBMED:9670025) ]. In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site, and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex [ (PUBMED:12242451) ].
Family alignment:
There are 2414 RPOL_N domains in 2413 proteins in SMART's nrdb database.
Click on the following links for more information.
Evolution (species in which this domain is found)
Taxonomic distribution of proteins containing RPOL_N domain.
This tree includes only several representative species. The complete taxonomic breakdown of all proteins with RPOL_N domain is also avaliable.
Click on the protein counts, or double click on taxonomic names to display all proteins containing RPOL_N domain in the selected taxonomic class.
Structural basis for the transition from initiation to elongation transcriptionin T7 RNA polymerase.
Science. 2002; 298: 1387-95
Display abstract
To make messenger RNA transcripts, bacteriophage T7 RNA polymerase (T7 RNAP)undergoes a transition from an initiation phase, which only makes short RNAfragments, to a stable elongation phase. We have determined at 2.1 angstromresolution the crystal structure of a T7 RNAP elongation complex with 30 basepairs of duplex DNA containing a "transcription bubble" interacting with a17-nucleotide RNA transcript. The transition from an initiation to an elongation complex is accompanied by a major refolding of the amino-terminal 300 residues.This results in loss of the promoter binding site, facilitating promoterclearance, and creates a tunnel that surrounds the RNA transcript after it peels off a seven-base pair heteroduplex. Formation of the exit tunnel explains theenhanced processivity of the elongation complex. Downstream duplex DNA binds tothe fingers domain, and its orientation relative to upstream DNA in theinitiation complex implies an unwinding that could facilitate formation of theopen promoter complex.
Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7lysozyme.
EMBO J. 1998; 17: 4101-13
Display abstract
The T7 RNA polymerase-T7 lysozyme complex regulates phage gene expression during infection of Escherichia coli. The 2.8 A crystal structure of the complex revealsthat lysozyme binds at a site remote from the polymerase active site, suggesting an indirect mechanism of inhibition. Comparison of the T7 RNA polymerasestructure with that of the homologous pol I family of DNA polymerases revealsidentities in the catalytic site but also differences specific to RNA polymerase function. The structure of T7 RNA polymerase presented here differs significantlyfrom a previously published structure. Sequence similarities between phage RNApolymerases and those from mitochondria and chloroplasts, when interpreted in thecontext of our revised model of T7 RNA polymerase, suggest a conserved fold.
