Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864
Letunic et al. (2012) Nucleic Acids Res , doi:10.1093/nar/gkr931

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RPOLA_N RNA polymerase I subunit A N-terminus

SMART accession number:	SM00663
Description:
Interpro abstract (IPR006592):	The task of transcribing nuclear genes is shared between three RNA polymerases in eukaryotes: RNA polymerase (pol) I synthesizes the large rRNA, pol II synthesizes mRNA and pol III synthesizes tRNA and 5S rRNA [(PUBMED:10684922)]. Pol I transcription is localised to discrete sites called nucleoli; these can be likened to ribosome factories, in which rRNA is synthesised by pol I in the fibrillar centres and then processed and assembled into ribosomes in the surrounding granular regions [(PUBMED:8689574)]. Prokaryotes, in contrast, posses a single RNA polymerase, with transcription being controlled by the particular signam factor interacting with the catalytic core. This entry describes an N-terminal conserved region which can be found in the largest subunits of prokaryoptic and eukaryotic RNA polymerases.
GO process:	transcription, DNA-dependent (GO:0006351)
GO function:	DNA-directed RNA polymerase activity (GO:0003899), DNA binding (GO:0003677)
Family alignment:	View or CHROMA formatCLUSTALW formatMSF formatFASTA formatPIR format

There are 4464 RPOLA_N domains in 4464 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Click on to expand nodes. To display all proteins with a RPOLA_N domain in a specific node, click on it.

  This tree shows only several representative species. The complete taxonomic breakdown of all proteins with RPOLA_N domain is also avaliable.

  Useful shortcuts: Expand all nodes or Collapse tree
  Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes

• Cellular role (predicted cellular role)

• Cellular role: transcription
  

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Severinov K et al.
  • Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the beta and beta' subunits of Escherichia coli RNA polymerase.
  • J Biol Chem. 1996; 271: 27969-74
  • Display abstract

  • The beta and beta' subunits of Escherichia coli DNA-dependent RNA polymerase are highly conserved throughout eubacterial and eukaryotic kingdoms. However, in some archaebacteria and chloroplasts, the corresponding sequences are "split" into smaller polypeptides that are encoded by separate genes. To test if such split sites can be accommodated into E. coli RNA polymerase, subunit fragments encoded by the segments of E. coli rpoB and rpoC genes corresponding to archaebacterial and chloroplast split subunits were individually overexpressed. The purified fragments, when mixed in vitro with complementing intact RNA polymerase subunits, yielded an active enzyme capable of catalyzing the phosphodiester bond formation. Thus, the large subunits of eubacteria and eukaryotes are composed of independent structural modules corresponding to the smaller subunits of archaebacteria and chloroplasts.

• Metabolism (metabolic pathways involving proteins which contain this domain)

• % proteins involved KEGG pathway ID Description 100.00 map03020 RNA polymerase This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with RPOLA_N domain which could be assigned to a KEGG orthologous group, and not all proteins containing RPOLA_N domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of RPOLA_N domains in PDB

  PDB code	Main view	Title
  1hqm		Crystal structure of thermus aquaticus core rna polymerase- includes complete structure with side-chains (except for disordered regions)-further refined from original deposition-contains additional sequence information
  1i3q		Rna polymerase ii crystal form i at 3.1 a resolution
  1i50		Rna polymerase ii crystal form ii at 2.8 a resolution
  1i6h		Rna polymerase ii elongation complex
  1i6v		Thermus aquaticus core rna polymerase-rifampicin complex
  1iw7		Crystal structure of the rna polymerase holoenzyme from thermus thermophilus at 2.6a resolution
  1k83		Crystal structure of yeast rna polymerase ii complexed with the inhibitor alpha amanitin
  1l9u		Thermus aquaticus rna polymerase holoenzyme at 4 a resolution
  1l9z		Thermus aquaticus rna polymerase holoenzyme/fork-junction promoter dna complex at 6.5 a resolution
  1nik		Wild type rna polymerase ii
  1nt9		Complete 12-subunit rna polymerase ii
  1pqv		Rna polymerase ii-tfiis complex
  1r5u		Rna polymerase ii tfiib complex
  1r9s		Rna polymerase ii strand separated elongation complex, matched nucleotide
  1r9t		Rna polymerase ii strand separated elongation complex, mismatched nucleotide
  1sfo		Rna polymerase ii strand separated elongation complex
  1smy		Structural basis for transcription regulation by alarmone ppgpp
  1twa		Rna polymerase ii complexed with atp
  1twc		Rna polymerase ii complexed with gtp
  1twf		Rna polymerase ii complexed with utp at 2.3 a resolution
  1twg		Rna polymerase ii complexed with ctp
  1twh		Rna polymerase ii complexed with 2'datp
  1wcm		Complete 12-subunit rna polymerase ii at 3.8 ang
  1y1v		Refined rna polymerase ii-tfiis complex
  1y1w		Complete rna polymerase ii elongation complex
  1y1y		Rna polymerase ii-tfiis-dna/rna complex
  1y77		Complete rna polymerase ii elongation complex with substrate analogue gmpcpp
  1ynj		Taq rna polymerase-sorangicin complex
  1ynn		Taq rna polymerase-rifampicin complex
  1zyr		Structure of thermus thermophilus rna polymerase holoenzyme in complex with the antibiotic streptolydigin
  2a68		Crystal structure of the t. thermophilus rna polymerase holoenzyme in complex with antibiotic rifabutin
  2a69		Crystal structure of the t. thermophilus rna polymerase holoenzyme in complex with antibiotic rifapentin
  2a6e		Crystal structure of the t. thermophilus rna polymerase holoenzyme
  2a6h		Crystal structure of the t. thermophilus rna polymerase holoenzyme in complex with antibiotic sterptolydigin
  2b63		Complete rna polymerase ii-rna inhibitor complex
  2b8k		12-subunit rna polymerase ii
  2be5		Crystal structure of the t. thermophilus rna polymerase holoenzyme in complex with inhibitor tagetitoxin
  2cw0		Crystal structure of thermus thermophilus rna polymerase holoenzyme at 3.3 angstroms resolution
  2e2h		Rna polymerase ii elongation complex at 5 mm mg2+ with gtp
  2e2i		Rna polymerase ii elongation complex in 5 mm mg+2 with 2'- dgtp
  2e2j		Rna polymerase ii elongation complex in 5 mm mg+2 with gmpcpp
  2gho		Recombinant thermus aquaticus rna polymerase for structural studies
  2ja5		Cpd lesion containing rna polymerase ii elongation complex a
  2ja6		Cpd lesion containing rna polymerase ii elongation complex b
  2ja7		Cpd lesion containing rna polymerase ii elongation complex c
  2ja8		Cpd lesion containing rna polymerase ii elongation complex d
  2nvq		Rna polymerase ii elongation complex in 150 mm mg+2 with 2'dutp
  2nvt		Rna polymerase ii elongation complex in 150 mm mg+2 with gmpcpp
  2nvx		Rna polymerase ii elongation complex in 5 mm mg+2 with 2'- dutp
  2nvy		Rna polymerase ii form ii in 150 mm mn+2
  2nvz		Rna polymerase ii elongation complex with utp, updated 11/2006
  2o5i		Crystal structure of the t. thermophilus rna polymerase elongation complex
  2o5j		Crystal structure of the t. thermophilus rnap polymerase elongation complex with the ntp substrate analog
  2pmz		Archaeal rna polymerase from sulfolobus solfataricus
  2ppb		Crystal structure of the t. thermophilus rnap polymerase elongation complex with the ntp substrate analog and antibiotic streptolydigin
  2r7z		Cisplatin lesion containing rna polymerase ii elongation complex
  2r92		Elongation complex of rna polymerase ii with artificial rdrp scaffold
  2r93		Elongation complex of rna polymerase ii with a hepatitis delta virus-derived rna stem loop
  2vum		Alpha-amanitin inhibited complete rna polymerase ii elongation complex
  2waq		The complete structure of the archaeal 13-subunit dna- directed rna polymerase
  2wb1		The complete structure of the archaeal 13-subunit dna- directed rna polymerase
  2yu9		Rna polymerase ii elongation complex in 150 mm mg+2 with utp
  3cqz		Crystal structure of 10 subunit rna polymerase ii in complex with the inhibitor alpha-amanitin
  3dxj		Crystal structure of thermus thermophilus rna polymerase holoenzyme in complex with the antibiotic myxopyronin
  3eql		Crystal structure of the t. thermophilus rna polymerase holoenzyme in complex with antibiotic myxopyronin
  3fki		12-subunit rna polymerase ii refined with zn-sad data
  3gtg		Backtracked rna polymerase ii complex with 12mer rna
  3gtj		Backtracked rna polymerase ii complex with 13mer rna
  3gtk		Backtracked rna polymerase ii complex with 18mer rna
  3gtl		Backtracked rna polymerase ii complex with 13mer with g<>u mismatch
  3gtm		Co-complex of backtracked rna polymerase ii with tfiis
  3gto		Backtracked rna polymerase ii complex with 15mer rna
  3gtp		Backtracked rna polymerase ii complex with 24mer rna
  3gtq		Backtracked rna polymerase ii complex induced by damage
  3h0g		Rna polymerase ii from schizosaccharomyces pombe
  3h3v		Yeast rnap ii containing poly(a)-signal sequence in the active site
  3hkz		The x-ray crystal structure of rna polymerase from archaea
  3hou		Complete rna polymerase ii elongation complex i with a t-u mismatch
  3hov		Complete rna polymerase ii elongation complex ii
  3how		Complete rna polymerase ii elongation complex iii with a t-u mismatch and a frayed rna 3'-uridine
  3hox		Complete rna polymerase ii elongation complex v
  3hoy		Complete rna polymerase ii elongation complex vi
  3hoz		Complete rna polymerase ii elongation complex iv with a t-u mismatch and a frayed rna 3'-guanine
  3i4m		8-oxoguanine containing rna polymerase ii elongation complex d
  3i4n		8-oxoguanine containing rna polymerase ii elongation complex e
  3iyd		Three-dimensional em structure of an intact activator- dependent transcription initiation complex
  3k1f		Crystal structure of rna polymerase ii in complex with tfiib
  3k7a		Crystal structure of an rna polymerase ii-tfiib complex

• Links (links to other resources describing this domain)

• PFAM	RNA_pol_A
  INTERPRO	IPR006592

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