RPOLDRNA polymerases D |
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| SMART accession number: | SM00662 |
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| Description: | DNA-directed RNA polymerase subunit D and bacterial alpha chain |
| Interpro abstract (IPR011263): | 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-templated (GO:0006351) |
| GO function: | DNA-directed 5'-3' RNA polymerase activity (GO:0003899) |
| Family alignment: |
There are 23040 RPOLD domains in 23040 proteins in SMART's nrdb database.
Click on the following links for more information.
- Evolution (species in which this domain is found)
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Taxonomic distribution of proteins containing RPOLD domain.
This tree includes only several representative species. The complete taxonomic breakdown of all proteins with RPOLD domain is also avaliable.
Click on the protein counts, or double click on taxonomic names to display all proteins containing RPOLD domain in the selected taxonomic class.
- Cellular role (predicted cellular role)
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Cellular role: transcription
- Literature (relevant references for this domain)
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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)
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% 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 A 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 2y0s 
Crystal structure of Sulfolobus shibatae RNA polymerase in P21 space group 2yu9 
RNA polymerase II elongation complex in 150 mm MG+2 with UTP 3aoh 
RNA polymerase-Gfh1 complex (Crystal type 1) 3aoi 
RNA polymerase-Gfh1 complex (Crystal type 2) 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 3j0k 
Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly 3j1n 
Cryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head module 3k1f 
Crystal structure of RNA Polymerase II in complex with TFIIB 3k7a 
Crystal Structure of an RNA polymerase II-TFIIB complex 3lu0 
Molecular model of Escherichia coli core RNA polymerase 3m3y 
RNA polymerase II elongation complex C 3m4o 
RNA polymerase II elongation complex B 3po2 
Arrested RNA Polymerase II elongation complex 3po3 
Arrested RNA Polymerase II reactivation intermediate 3qt1 
RNA polymerase II variant containing A Chimeric RPB9-C11 subunit 3rzd 
RNA Polymerase II Initiation Complex with a 5-nt RNA 3rzo 
RNA Polymerase II Initiation Complex with a 4-nt RNA 3s14 
RNA Polymerase II Initiation Complex with a 6-nt RNA 3s15 
RNA Polymerase II Initiation Complex with a 7-nt RNA 3s16 
RNA Polymerase II Initiation Complex with an 8-nt RNA 3s17 
RNA Polymerase II Initiation Complex with a 9-nt RNA 3s1m 
RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 1) 3s1n 
RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 2) 3s1q 
RNA Polymerase II Initiation Complex with a 5-nt 3'-deoxy RNA soaked with ATP 3s1r 
RNA Polymerase II Initiation Complex with a 5-nt 3'-deoxy RNA soaked with GTP 3s2d 
RNA Polymerase II Initiation Complex with a 5-nt RNA containing a 5Br-U 3s2h 
RNA Polymerase II Initiation Complex with a 6-nt RNA containing a 2[prime]-iodo ATP 3wod 
RNA polymerase-gp39 complex 4a3b 
RNA Polymerase II initial transcribing complex with a 4nt DNA-RNA hybrid 4a3c 
RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid 4a3d 
RNA Polymerase II initial transcribing complex with a 6nt DNA-RNA hybrid 4a3e 
RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid and soaked with AMPCPP 4a3f 
RNA Polymerase II initial transcribing complex with a 6nt DNA-RNA hybrid and soaked with AMPCPP 4a3g 
RNA Polymerase II initial transcribing complex with a 2nt DNA-RNA hybrid 4a3i 
RNA Polymerase II binary complex with DNA 4a3j 
RNA Polymerase II initial transcribing complex with a 2nt DNA-RNA hybrid and soaked with GMPCPP 4a3k 
RNA Polymerase II initial transcribing complex with a 7nt DNA-RNA hybrid 4a3l 
RNA Polymerase II initial transcribing complex with a 7nt DNA-RNA hybrid and soaked with AMPCPP 4a3m 
RNA Polymerase II initial transcribing complex with a 4nt DNA-RNA hybrid and soaked with AMPCPP 4a93 
RNA Polymerase II elongation complex containing a CPD Lesion 4ayb 
RNAP at 3.2Ang 4bbr 
Structure of RNA polymerase II-TFIIB complex 4bbs 
Structure of an initially transcribing RNA polymerase II-TFIIB complex 4bxx 
Structures of RNA polymerase II complexes with Bye1, a chromatin- binding PHF3 DIDO homologue 4bxz 
RNA Polymerase II-Bye1 complex 4by1 
elongating RNA Polymerase II-Bye1 TLD complex soaked with AMPCPP 4by7 
elongating RNA Polymerase II-Bye1 TLD complex 4c2m 
Structure of RNA polymerase I at 2.8 A resolution 4c3h 
Structure of 14-subunit RNA polymerase I at 3.27 A resolution, crystal form C2-93 4c3i 
Structure of 14-subunit RNA polymerase I at 3.0 A resolution, crystal form C2-100 4c3j 
Structure of 14-subunit RNA polymerase I at 3.35 A resolution, crystal form C2-90 4g7h 
Crystal structure of Thermus thermophilus transcription initiation complex 4g7o 
Crystal structure of Thermus thermophilus transcription initiation complex containing 2 nt of RNA 4g7z 
Crystal structure of Thermus thermophilus transcription initiation complex containing 5-BrU at template-strand position +1 4gzy 
Crystal structures of bacterial RNA Polymerase paused elongation complexes 4gzz 
Crystal structures of bacterial RNA Polymerase paused elongation complexes 4jk1 
X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with Guanosine tetraphosphate (ppGpp) 4jk2 
X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with guanosine pentaphosphate (pppGpp) 4jkr 
Crystal Structure of E. coli RNA Polymerase in complex with ppGpp 4kmu 
X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin 4kn4 
X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Benzoxazinorifamycin-2b 4kn7 
X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Benzoxazinorifamycin-2c 4ljz 
Crystal Structure Analysis of the E.coli holoenzyme 4lk0 
Crystal Structure Analysis of the E.coli holoenzyme/T7 Gp2 complex 4lk1 
Crystal Structure Analysis of the E.coli holoenzyme 4llg 
Crystal Structure Analysis of the E.coli holoenzyme/Gp2 complex 4mex 
Crystal structure of Escherichia coli RNA polymerase in complex with salinamide A 4mey 
Crystal structure of Escherichia coli RNA polymerase holoenzyme 4mq9 
Crystal structure of Thermus thermophilus RNA polymerase holoenzyme in complex with GE23077 4noi 
2.17 Angstrom Crystal Structure of DNA-directed RNA Polymerase Subunit Alpha from Campylobacter jejuni. 4oin 
Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077 4oio 
Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation 4oip 
Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077, ATP, and CMPcPP 4oiq 
Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077 and rifampicin 4oir 
Crystal structure of Thermus thermophilus RNA polymerase transcription initiation complex soaked with GE23077 and rifamycin SV 4q4z 
4Q4Z 4q5s 
4Q5S 4qiw 
4QIW 4qjv 
4QJV 4s20 
4S20 4v1m 
4V1M 4v1n 
4V1N 4v1o 
4V1O 4v8s 
4V8S 4wqs 
4WQS 4wqt 
4WQT 4x67 
4X67 4x6a 
4X6A 4xln 
4XLN 4xlp 
4XLP 4xlq 
4XLQ 4xlr 
4XLR 4xls 
4XLS 4xsx 
4XSX 4xsy 
4XSY 4xsz 
4XSZ 4y52 
4Y52 4y7n 
4Y7N 4yfk 
4YFK 4yfn 
4YFN 4yfx 
4YFX 4yg2 
4YG2 4yln 
4YLN 4ylo 
4YLO 4ylp 
4YLP 4ym7 
4YM7 4zh2 
4ZH2 4zh3 
4ZH3 4zh4 
4ZH4 5byh 
5BYH 5c3e 
5C3E 5c44 
5C44 5c4a 
5C4A 5c4j 
5C4J 5c4x 
5C4X 5d4c 
5D4C 5d4d 
5D4D 5d4e 
5D4E 5e17 
5E17 5e18 
5E18 5ezk 
5EZK 5fj8 
5FJ8 5fj9 
5FJ9 5fja 
5FJA 5flm 
5FLM 5fmf 
5FMF 5fyw 
5FYW 5fz5 
5FZ5 5g5l 
5G5L 5i2d 
5I2D 5ip7 
5IP7 5ip9 
5IP9 5ipl 
5IPL 5ipm 
5IPM 5ipn 
5IPN 5iy6 
5IY6 5iy7 
5IY7 5iy8 
5IY8 5iy9 
5IY9 5iya 
5IYA 5iyb 
5IYB 5iyc 
5IYC 5iyd 
5IYD 5m3f 
5M3F 5m3m 
5M3M 5sva 
5SVA 5tmc 
5TMC 5tmf 
5TMF - Links (links to other resources describing this domain)
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INTERPRO IPR011263 PFAM RNA_pol_A_bac