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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RPOLD RNA polymerases D

SMART accession number:	SM00662
Description:	DNA-directed RNA polymerase subunit D and bacterial alpha chain
Interpro abstract (IPR011263):	DNA-directed RNA polymerases EC 2.7.7.6 (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. 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, and plays a direct role in promoter recognition [(PUBMED:10972792)]. In eukaryotes, RNA polymerase (RNAP) II is responsible for all mRNA synthesis. RNAP-II consists of 12 subunits, where subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the bacterial RpoA homodimer [(PUBMED:12860379)]. Archaeal RNAP closely resembles eukaryotic RNAP-II, and is composed of 12 subunits, of which D and L form a heterodimer resembling the Rpb3/Rpb11 and RpoA/RpoA dimers [(PUBMED:12694606)]. The bacterial RpoA, eukaryotic Rpb3 and archaeal D subunits share sequence and structural motifs, and can be placed into a single family. These subunits also have unique sequence motifs, especially at their C-terminal ends, which are involved in promoter specificity, for example the CTD of the bacterial RNAP alpha subunit (IPR011260).
GO process:	transcription, DNA-dependent (GO:0006351)
GO function:	DNA-directed RNA polymerase activity (GO:0003899)
Family alignment:	View or CHROMA formatCLUSTALW formatMSF formatFASTA formatPIR format

There are 2512 RPOLD domains in 2512 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 RPOLD domain in a specific node, click on it.

  This tree shows only several representative species. The complete taxonomic breakdown of all proteins with RPOLD 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.

  • Pati UK, Weissman SM
  • The amino acid sequence of the human RNA polymerase II 33-kDa subunit hRPB 33 is highly conserved among eukaryotes.
  • J Biol Chem. 1990; 265: 8400-3
  • Display abstract

  • We have cloned and sequenced a cDNA of 1766 base pairs in length encoding the 275 amino acids of hRPB 33, the third largest subunit of human RNA polymerase II. The DNA was isolated by screening of a human lambda gt11 cDNA library with oligonucleotides designed on the basis of the amino acid residue analysis of the bovine material. The hRPB 33 amino acid sequence is highly conserved between Saccharomyces cerevisiae and human. Overall, 45% of the amino acid residues are identical with the yeast homologue RPB 3, and 65% of the amino acids are identical in the two major conserved regions at residues 0-103 and 151-197. hRPB 33 is also homologous to yeast RPC 5. The amino acid sequence of hRPB 33 showed no obvious homology with bacterial RNA polymerase or with any of its sigma factors.

  • Kolodziej P, Young RA
  • RNA polymerase II subunit RPB3 is an essential component of the mRNA transcription apparatus.
  • Mol Cell Biol. 1989; 9: 5387-94
  • Display abstract

  • To improve our understanding of RNA polymerase II, the gene that encodes its third-largest subunit, RPB3, was isolated from a lambda gt11 DNA library by using antibody probes. The RPB3 DNA sequence predicts a 318-amino-acid protein whose sequence was confirmed, in part, by microsequence analysis of the gel-purified RNA polymerase II subunit. RPB3 was found to be an essential single-copy gene that is tightly linked to HIS6 on chromosome IX. An RPB3 temperature-sensitive mutant that arrested growth after three to four generations at the restrictive temperature was isolated. When the mutant was shifted to the restrictive temperature, RNA polymerase II could no longer assemble, previously assembled functional enzyme was depleted, and mRNA levels were consequently reduced. These results demonstrate that RPB3 is an essential component of the mRNA transcription apparatus. Finally, the RPB3 protein is similar in sequence and length to RPC5, a subunit common to RNA polymerases I and III, suggesting that these subunits may play similar roles in RNA polymerases I, II, and III.

• 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 RPOLD domain which could be assigned to a KEGG orthologous group, and not all proteins containing RPOLD 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 RPOLD domains in PDB

  PDB code	Main view	Title
  1bdf		Structure of escherichia coli rna polymerase alpha subunit n-terminal domain
  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
  2pa8		X-ray crystal structure of the d/l subcomplex of the sulfolobus solfataricus rna polymerase
  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_bac
  INTERPRO	IPR011263

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