2.7.7.6: DNA-directed RNA polymerase
This is an abbreviated version!
For detailed information about DNA-directed RNA polymerase, go to the full flat file.
Word Map on EC 2.7.7.6
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2.7.7.6
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chromatin
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histone
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rrna
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strand
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rnaps
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nucleosome
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tata
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drosophila
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pausing
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pre-mrnas
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tbp
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nucleolar
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bacteriophage
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polyadenylation
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single-stranded
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cyclin-dependent
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holoenzyme
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cyclin
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spacers
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helicase
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fidelity
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polya
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coactivator
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protein-coding
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transactivation
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adenovirus
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xenopus
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ribonucleoproteins
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sequence-specific
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stall
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pause
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chip-seq
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vaccinia
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multisubunit
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ribozyme
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heptapeptide
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duplex
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h3k4me3
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spliceosome
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nucleoplasm
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run-on
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supercoiled
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trimethylation
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subcomplexes
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exonuclease
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heterochromatin
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translesion
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medicine
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primase
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molecular biology
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analysis
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diagnostics
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drug development
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misincorporation
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proofread
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synthesis
- 2.7.7.6
- chromatin
- histone
- rrna
- strand
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rnaps
- nucleosome
- tata
- drosophila
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pausing
- pre-mrnas
- tbp
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nucleolar
- bacteriophage
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polyadenylation
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single-stranded
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cyclin-dependent
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holoenzyme
- cyclin
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spacers
- helicase
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fidelity
- polya
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coactivator
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protein-coding
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transactivation
- adenovirus
- xenopus
- ribonucleoproteins
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sequence-specific
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stall
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pause
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chip-seq
- vaccinia
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multisubunit
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ribozyme
- heptapeptide
- duplex
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h3k4me3
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spliceosome
- nucleoplasm
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run-on
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supercoiled
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trimethylation
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subcomplexes
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exonuclease
- heterochromatin
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translesion
- medicine
- primase
- molecular biology
- analysis
- diagnostics
- drug development
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misincorporation
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proofread
- synthesis
Reaction
Synonyms
C RNA formation factors, chloroplast soluble RNA polymerase, deoxyribonucleic acid-dependent ribonucleic acid polymerase, DNA-dependent ribonucleate nucleotidyltransferase, DNA-dependent RNA nucleotidyltransferase, DNA-dependent RNA polymerase, DNA-dependent RNA polymerase I, DNA-dependent RNA polymerase III, DNA-dependent RNAP, h-mtRNAP, K1E RNAP, mitochondrial RNA polymerase, mitoRNAP, More, mtRNAP, multi-subunit RNA polymerase, nucleotidyltransferase, ribonucleate, plastid RNA polymerase, plastid-encoded polymerase, plastid-encoded RNA polymerase, Pol I, Pol II, pol III, Pol IIIalpha, Pol IIIbeta, Pol IV, Pol V, polI, PolIII, POLRMT, ribonucleate nucleotidyltransferase, ribonucleate polymerase, ribonucleic acid formation factors, C, ribonucleic acid nucleotidyltransferase, ribonucleic acid polymerase, ribonucleic acid transcriptase, ribonucleic polymerase, ribonucleic transcriptase, rifampicin-resistant RNA polymerase, RNA formation factors, C, RNA nucleotidyltransferase, RNA nucleotidyltransferase (DNA-directed), RNA pol III, RNA polymerase, RNA polymerase core enzyme, RNA polymerase I, RNA polymerase II, RNA polymerase II complex, RNA polymerase III, RNA polymerase III complex, RNA transcriptase, RNAP, RNAP core enzyme, RNAP I, RNAP II, RNAP III, RNAP sigma70, RNAP-II, RNAP2, RNAPII, RPO, rpo1N, Rpo41, RpoA, RpoD, RpoS, RpoT, Saci_0834, sigma38 RNA polymerase, sigmaS-containing RNA polymerase, T7 RNA polymerase, T7 RNAP, T7-like RNA polymerase, Taq polymerase, transcriptase, YonO
ECTree
2.7.7.6 DNA-directed RNA polymeraseAdvanced search results
results (
results (Subunits
Subunits on EC 2.7.7.6 - DNA-directed RNA polymerase
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SUBUNIT 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
decamer
dodecamer
heterotrimer
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the three subunits, PB1, PB2 and PA, are all required for both transcription and replication, PB1 carries the polymerase active site, PB2 includes the capped-RNA recognition domain, and PA, whose C-terminal domain consists of 13 alpha-helices and 9 beta-strands, is involved in assembly of the functional complex. The subunit interface is important for virla replication, overview
monomer
multimer
oligomer
additional information
?
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x * 171000 + x * 124000 + x * 66000 + x * 52000 + x * 41000, SDS-PAGE
?
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x * 185000 + x * 125000 + x * 47000 + x * 30000 + x * 93000, SDS-PAGE
?
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betax,beta,sigma,alpha, x * 160000 + x * 145000 + x * 85000 + x * 40000, SDS-PAGE
?
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the most probably subunit structure for the enzyme is the following: 154000 + 104000 + 77000 + 64000 + 52000 + 48000 + 46000 + 45000 + 39000
?
Leishmania sp. UR6
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the most probably subunit structure for the enzyme is the following: 154000 + 104000 + 77000 + 64000 + 52000 + 48000 + 46000 + 45000 + 39000
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?
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x * 171000 + x * 124000 + x * 66000 + x * 52000 + x * 41000, SDS-PAGE
?
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x * 161000 + x * 134000 + x * 72000 + x * 41000 + x * 91000, SDS-PAGE
?
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x * 120000 + x * 110000 + x * 95000 + x * 84000 + x * 81000 + x * 75000 + x * 54000 + x * 51000 + x * 42000 + x * 35000, the 110000 Da polypeptide binds nucleoside triphosphates, the 42000 Da polypeptide cross-reacts with antiserum raised to the plastid endoded rpoA gene product, SDS-PAGE
?
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betax,betax,alphax,sigmax, x * 156000 + x * 151000 + x * 87000 + x * 42000, SDS-PAGE
?
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betax,betax,alphax,sigmax, x * 156000 + x * 151000 + x * 87000 + x * 42000, SDS-PAGE
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?
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betax,betax,sigmax,alphax, x * 148000 + x * 142000 + x * 85000 + x * 34500, SDS-PAGE
?
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x * 210000 + x * 150000 + x * 40000 + x * 34000 + x * 33000 + x * 25000 + x * 20000 + x * 16000 + x * 15000 + x * 13500 + x * 13000, the enzyme contains more than eleven polypeptides, SDS-PAGE
?
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x * 25608, RpoE2, sequence calculation, x * 20103, RpoE3, sequence calculation
?
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x * 25608, RpoE2, sequence calculation, x * 20103, RpoE3, sequence calculation
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?
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x * 146000, beta and beta comigrate, + x * 105000, main sigma factor, + x * 40000, alpha, SDS-PAGE
?
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x * 171000 + x * 124000 + x * 66000 + x * 52000 + x * 41000, SDS-PAGE
?
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x * 190000 + x * 145000 + x * 72000 + x * 38000, SDS-PAGE
?
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beta,beta,sigma,alpha occur with a stoichiometric ratio of 1:1:1:2, x * 184000 + x * 141000 + x * 55000 + x * 45000, SDS-PAGE
?
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betax,betax,alphax,sigmax,sigmax, x * 170000 + x * 140000 + x * 40000 + x * 90000 + x * 60000, SDS-PAGE
?
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betax,betax,alpha,x,sigmax, x * 140000 + x * 170000 + x * 40000 + x * 92000, SDS-PAGE
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Thermus thermophilus HB8 / ATCC 27634 / DSM 579
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betax,betax,alpha,x,sigmax, x * 140000 + x * 170000 + x * 40000 + x * 92000, SDS-PAGE
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?
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
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betax,betax,alphax,sigmax,sigmax, x * 170000 + x * 140000 + x * 40000 + x * 90000 + x * 60000, SDS-PAGE
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decamer
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1 * 122000 + 1 * 101000 + 1 * 44000 + 1 * 32000 + 1 * 24000 + 1 * 17500 + 1 * 13800 + 4 * 11800 + 1 * 11200 + 1 * 10800, SDS-PAGE
dodecamer
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the Rpb2 subunit of RNAP II combines with the Rpb1 subunit to form the RNAP II active site. RNAP II is isolated as a 12 subunit enzyme, Rpb1-Rpb12
dodecamer
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the Rpb2 subunit of RNAP II combines with the Rpb1 subunit to form the RNAP II active site. RNAP II is isolated as a 12 subunit enzyme, Rpb1-Rpb12
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monomer
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the enzyme consists of three distinct regions, a catalytic C-terminal polymerase domain (residues 648-1230), an N-terminal domain (residues 369-647) and an N-terminal extension (residues 1-368), domain architecture, overview. The POLRMT C-terminal domain is characteristic of the Pol I family of nucleic acid polymerases, typically described as resembling the shape of a cupped right hand, containing the fingers, palm and thumb subdomains. The palm subdomain contains several key structural motifs that are highly conserved among the different classes of nucleic acid polymerases. The N-terminal extension contains the mitochondrial targeting sequence (residues 1-41), a large, flexible region of unknown structure (residues 42-217) and a pentatricopeptide repeat domain (residues 218-368). The pentatricopeptide repeat domain is connected to the N-terminal domain via a short proline-rich linker region that likely functions as a spacer connecting the two domains. The pentatricopeptide repeat domain consists of two tandem PPR motifs, the domnain contains nine alpha-helices of which four comprise the pentatricopeptide repeat motifs
multimer
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bacterial RNAP is a multisubunit enzyme and consists of a core polymerase containing the beta, beta' , and two alpha subunits, together with one or more omega subunits, and a dissociable specificity factor sigma
multimer
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x * 130000, beta-subunit, plus x * 140000, beta'-subunit, SDS-PAGE
multimer
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bacterial RNAP is a multisubunit enzyme and consists of a core polymerase containing the beta, beta' , and two alpha subunits, together with one or more omega subunits, and a dissociable specificity factor sigma
oligomer
Autographa californica M nucleopolyhedrovirus
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the viral RNA polymerase is composed of four proteins: Late Expression Factor-4 (LEF-4), LEF-8, LEF-9, and P47. Associations are observed between LEF-9 and P47, LEF-4 and P47, and LEF-8 and P47. LEF-4 and LEF-8 do not coimmunoprecipitate but coimmunoprecipitated in the presence of P47, suggesting that they do not associate directly. A weak association is observed between LEF-4 and LEF-9. LEF-8, LEF-9, and P47 have the ability to self-associate
oligomer
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beta',beta,sigma,alpha. Subunit stoichiometry is 1:1:1:2, x * 157000 + x * 148000 + x * 87000 + 2 * x * 45000, SDS-PAGE
oligomer
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structure and modeling of the multi-subunit enzyme complex, RNAP subunits can be divided into three groups concerned with catalysis, assembly of the catalytic subunits and auxiliary functions, overview. The large A and B subunits are split into two polypeptides, A'/A'' and B''/B' according to size, they harbour the binding sites for substrate NTPs, duplex DNA template and a 9 bp DNA-RNA hybrid, and provide the catalytic centre, including three catalytic aspartic acid residues and two Mg2+ ions
oligomer
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RNAPII structure and modeling of the multi-subunit enzyme complex, RNAP subunits can be divided into three groups concerned with catalysis, assembly of the catalytic subunits and auxiliary functions, overview
oligomer
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RNA polymerase III contains seventeen subunits. The Schizosaccharomyces pombe subunits are expressed in Saccharomyces cerevisiae null mutants and tested for growth. Ten core subunits show heterospecific complementation, but the two largest catalytic subunits (Rpc1 and Rpc2) and all five RNA polymerase III-specific subunits (Rpc82, Rpc53, Rpc37, Rpc34 and Rpc31) are non-functional. Three highly conserved RNA polymerase III-specific domains are found in the twelve-subunit core structure. They correspond to the Rpc17-Rpc25 dimer, involved in transcription initiation, to an N-terminal domain of the largest subunit Rpc1 important to anchor Rpc31, Rpc34 and Rpc82, and to a C-terminal domain of Rpc1 that presumably holds Rpc37, Rpc53 and their Rpc11 partner
oligomer
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alpha2betabeta'omega structure and modeling of the multi-subunit enzyme complex, RNAP subunits can be divided into three groups concerned with catalysis, assembly of the catalytic subunits and auxiliary functions, overview
additional information
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secondary structure and organization of multi-subunit DNA-dependent RNA polymerases, overview. The Rpb8/G RNA polymerase subunit is restricted to eukaryotes and Crenarchaea
additional information
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secondary structure and organization of multi-subunit DNA-dependent RNA polymerases, overview. The Rpb8/G RNA polymerase subunit is restricted to eukaryotes and Crenarchaea
additional information
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components of the RNA polymerase and their molecular weights determined by SDS-PAGE
additional information
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components of the RNA polymerase and their molecular weights determined by SDS-PAGE
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additional information
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secondary structure and organization of multi-subunit DNA-dependent RNA polymerases, overview. The Rpb8/G RNA polymerase subunit is restricted to eukaryotes and Crenarchaea
additional information
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dimer-monomer formation is reversible and the equilibrium depends on the ionic strength of the medium. At high ionic strength the enzyme dissociates to a monomeric form
additional information
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binding of the sigma70 subunit to the core enzyme induces conformational changes in a single-stranded DNA binding region of the protein. As a consequence of these conformational changes, sigma70 subunit gains the specificity for the nontemplate strand of the melted region in the open complex
additional information
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the core of the procaryotic RNAP comprises five subunits
additional information
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conformational plasticity of the active center and importance of the bridge helix structure for enzyme activity, overview
additional information
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secondary structure and organization of multi-subunit DNA-dependent RNA polymerases, overview. The Rpb8/G RNA polymerase subunit is restricted to eukaryotes and Crenarchaea
additional information
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RNAP contains the vegetative sigma subunit sigma70 (RpoD) and/or the flagellar sigma factor sigma28 (FliA)
additional information
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existence of two possible conformers: E and E that are in rapid equilibrium. Both forms can form the quarternary complex, but only the E form is capable of catalyzing phosphodiester bond formation
additional information
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subunits with molecular weights of 60 kDa and 45 kDa and a subunit with a molecular weight of 52 kDa (which is probably one of the basal transcription factors of RNA polymerase III) are modified in the composition of the enzyme isolated from human cells. The three subunits are simultaneously phosphorylated and glycosylated
additional information
the gene locus for the largest subunit is identified and its primary structure is determined
additional information
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the gene locus for the largest subunit is identified and its primary structure is determined
additional information
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secondary structure and organization of multi-subunit DNA-dependent RNA polymerases, overview. The Rpb8/G RNA polymerase subunit is restricted to eukaryotes and Crenarchaea. The enzyme lacks the G and M polypeptides
additional information
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3D structure of the RNA polymerase from the mitochondrial plasmid is T7 polymerase-like, modeling using molecular mechanics and molecular dynamics, overview
additional information
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subunits with molecular weights of 49 kDa and 42 kDa and a subunit with a molecular weight of 45 kDa (which is probably a component of the basal transcription factor of RNA polymerase III, since it is not identified in the mouse enzyme) are modified in the composition of the enzyme isolated from mouse fibroblasts. The two subunits are simultaneously phosphorylated and glycosylated (glycosylation by O-N-acetylglucosamine residues)
additional information
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secondary structure and organization of multi-subunit DNA-dependent RNA polymerases, overview. The Rpb8/G RNA polymerase subunit is restricted to eukaryotes and Crenarchaea. The enzyme lacks the G subunit
additional information
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secondary structure and organization of multi-subunit DNA-dependent RNA polymerases, overview. The Rpb8/G RNA polymerase subunit is restricted to eukaryotes and Crenarchaea
additional information
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subunit RpoS of RNA polymerase is a central regulator which governs the expression of a host of stationary phase-induced and osmotically regulated genesin gram-negative bacteria.
additional information
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subunit RpoS of RNA polymerase is a central regulator which governs the expression of a host of stationary phase-induced and osmotically regulated genesin gram-negative bacteria.
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additional information
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secondary structure and organization of multi-subunit DNA-dependent RNA polymerases, overview. The Rpb8/G RNA polymerase subunit is restricted to eukaryotes and Crenarchaea
additional information
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conformational plasticity of the active center and importance of the bridge helix structure for enzyme activity, overview
additional information
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secondary structure and organization of multi-subunit DNA-dependent RNA polymerases, overview. The Rpb8/G RNA polymerase subunit is restricted to eukaryotes and Crenarchaea. The enzyme lacks the G subunit
additional information
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structure analysis, overview, the enzyme contains a subunit Rpo13 located at a groove between the H subunit and the clamp head domain of the A' subunit, model ing including the A' subunit jaw and clamp head domains and RpoG and Rpo13, overview
additional information
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analysis of interaction sbetween the largest subunit Rpb1 and the other subunits, overview
additional information
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conformational plasticity of the active center and importance of the bridge helix structure for enzyme activity, overview
additional information
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detailed RNAPII structure study in different comformations, e.g. concerning the trigger loop, using crystal structures, the collective set of all normal modes describes enzyme flexibility as a function of residue in terms of root mean square fluctuations, RMSF values are directly related to crystallographic B-factors, enzyme motions described by individual modes, caclulations, overview
additional information
peptide regions that interact with regulatory factors are close to the Pol II surface and assume seemingly flexible loop structures, one is located in the TFIIF-interacting protrusion domain, the other is located in the TFIIE-interacting clamp domain, conformations, e.g. of the TFIIF-interacting Rpb2 protrusion, overview. Conformational movement and dynamics of fork loop-1 and -2. mechanism, overview
additional information
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secondary structure and organization of multi-subunit DNA-dependent RNA polymerases, overview. The Rpb8/G RNA polymerase subunit is restricted to eukaryotes and Crenarchaea
additional information
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the enzyme consists of three distinct regions, a catalytic C-terminal polymerase domain, an N-terminal domain and an N-terminal extension, a pentatricopeptide repeat domain is not present in the yeast enzyme
additional information
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the C-terminal domain (CTD) of RNA polymerase II in eukaryotes is comprised of tandemly repeating units of a conserved seven-amino acid sequence. DNA instability may play a role in regulating or maintaining C-terminal domain repeat number. 36 diverse Saccharomyces cerevisiae isolates reveal evidence of numerous past rearrangements within the DNA sequence that encodes the C-terminal domain, the total number of CTD repeats is relatively static (24-26 repeats in all strains), suggesting a balancing act between repeat expansion and contraction. Presence of DNA secondary structures, specifically G-quadruplex-like DNA,within the CTD coding region. Mutating PIF1, a G-quadruplex-specific helicase, results in increased CTD repeat length polymorphisms. RAD52 is necessary for CTD repeat expansion but not contraction, identifying a role for recombination in repeat expansion
additional information
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the C-terminal domain (CTD) of RNA polymerase II in eukaryotes is comprised of tandemly repeating units of a conserved seven-amino acid sequence. DNA instability may play a role in regulating or maintaining C-terminal domain repeat number. 36 diverse Saccharomyces cerevisiae isolates reveal evidence of numerous past rearrangements within the DNA sequence that encodes the C-terminal domain, the total number of CTD repeats is relatively static (24-26 repeats in all strains), suggesting a balancing act between repeat expansion and contraction. Presence of DNA secondary structures, specifically G-quadruplex-like DNA,within the CTD coding region. Mutating PIF1, a G-quadruplex-specific helicase, results in increased CTD repeat length polymorphisms. RAD52 is necessary for CTD repeat expansion but not contraction, identifying a role for recombination in repeat expansion
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additional information
enzyme structure analysis and comparison to the structures of Saccharomyces cerevisiae and human Pol IIs, overview
additional information
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enzyme structure analysis and comparison to the structures of Saccharomyces cerevisiae and human Pol IIs, overview
additional information
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at 0.5 M NH4CI the enzyme exists in the monomeric form
additional information
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peptide and subunit mapping for determination of the substrate binding site
additional information
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secondary structure and organization of multi-subunit DNA-dependent RNA polymerases, overview. The Rpb8/G RNA polymerase subunit is restricted to eukaryotes and Crenarchaea
additional information
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components of the RNA polymerase and their molecular weights determined by SDS-PAGE
additional information
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components of the RNA polymerase and their molecular weights determined by SDS-PAGE
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additional information
-
secondary structure and organization of multi-subunit DNA-dependent RNA polymerases, overview. The Rpb8/G RNA polymerase subunit is restricted to eukaryotes and Crenarchaea
additional information
-
components of the RNA polymerase and their molecular weights determined by SDS-PAGE
additional information
-
components of the RNA polymerase and their molecular weights determined by SDS-PAGE
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additional information
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conformational plasticity of the active center and importance of the bridge helix structure for enzyme activity, overview
additional information
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the bacterial RNAP uses a homodimeric assembly platform
additional information
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conformational plasticity of the active center and importance of the bridge helix structure for enzyme activity, overview
additional information
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subunits RPB5 and RPB6 localize to discrete subnuclear compartments and form part of different polymerase complexes. RNA interference mediated depletion of these discrete subunits abolishes class-specific transcription
additional information
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the PSi-C-terminal domain of large subunit RPB1 is essential for cell survivial and production of both SL RNA and mRNA, the Trypanosoma brucei enzyme lacks conserved heptapeptide sequence motifs found in most other eukaryotes
