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Enzyme Nomenclature
Information on EC 2.7.7.6 - DNA-directed RNA polymerase
for references in articles please use BRENDA:EC2.7.7.6
Word Map on EC 2.7.7.6
- 2.7.7.6
- chromatin
- histone
- viral
- rrna
-
nascent
-
rnaps
- nucleosome
- bacteriophage
- cap
-
nucleolar
-
pre-mrnas
-
cyclin-dependent
-
pausing
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polyadenylation
- xenopus
-
coactivator
-
double-stranded
-
holoenzyme
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single-stranded
- adenovirus
-
cyclins
-
transactivation
-
fidelity
- polya
-
exonuclease
- vaccinia
-
protein-coding
-
helicase
-
noncoding
-
ribonucleoproteins
-
stall
-
run-on
-
proofread
-
spliceosome
-
heptapeptide
-
subcomplexes
-
duplex
-
hyperphosphorylated
- heterochromatin
-
supercoiled
-
trimethylation
-
multisubunit
-
ribozyme
- nucleoplasm
-
pause
- diagnostics
- molecular biology
- drug development
- analysis
- synthesis
-
klenow
- medicine
-
translesion
-
misincorporation
-
polycomb
- primase
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Specify your search results
The enzyme appears in viruses and cellular organisms
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EC NUMBER 
COMMENTARY 
2.7.7.6
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RECOMMENDED NAME
GeneOntology No.
DNA-directed RNA polymerase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
nucleoside triphosphate + RNAn = diphosphate + RNAn+1
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nucleoside triphosphate + RNAn = diphosphate + RNAn+1
reaction mechanism
Q980R2 and P58192 and Q980R1 and P95989 and Q980A3 and Q9UXD9 and Q980L5 and Q980Q9 and Q97ZJ9 and Q980K0 and Q980Z8 and Q97ZX7 and Q980B8
nucleoside triphosphate + RNAn = diphosphate + RNAn+1
reaction mechanism
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
nucleotidyl group transfer
nucleotidyl group transfer
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-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
nucleoside-triphosphate:RNA nucleotidyltransferase (DNA-directed)
Catalyses DNA-template-directed extension of the 3'- end of an RNA strand by one nucleotide at a time. Can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. See also EC 2.7.7.19 (polynucleotide adenylyltransferase) and EC 2.7.7.48 (RNA-directed RNA polymerase).
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CAS REGISTRY NUMBER
COMMENTARY
9014-24-8
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
'Capsicum annum' phytoplasma
beta-subunit; gene rpoB, Capsicum annum from Serbia
UniProt
'Capsicum annum' phytoplasma Candidatus Phytoplasma solani
beta-subunit; gene rpoB, Capsicum annum from Serbia
UniProt
beta-subunit; gene rpoB, Catharanthus roseus from Maryland, USA
S5ZYX4
UniProt
beta-subunit; gene rpoB, Catharanthus roseus from Maryland, USA
S5ZYX4
UniProt
beta-subunit; gene rpoB, Euphorbia pulcherrima from USA
UniProt
beta-subunit; gene rpoB, Euphorbia pulcherrima from USA
UniProt
beta-subunit; gene rpoB, Fragaria x ananassa from Lithuania
S5ZYY2
UniProt
beta-subunit; gene rpoB, Fragaria x ananassa from Lithuania
S5ZYY2
UniProt
'Gomphocarpus physocarpus' phytoplasma
beta-subunit; gene rpoB, Gomphocarpus physocarpus from Australia
UniProt
'Gomphocarpus physocarpus' phytoplasma Candidatus Phytoplasma australiense
beta-subunit; gene rpoB, Gomphocarpus physocarpus from Australia
UniProt
beta-subunit; gene rpoB, Heracleum sosnowskyi from Lithuania
UniProt
beta-subunit; gene rpoB, Heracleum sosnowskyi from Lithuania
UniProt
'Lactuca sativa' phytoplasma
beta-subunit; gene rpoB, Lactuca sativa from Ohio, USA
UniProt
'Lactuca sativa' phytoplasma AYWB
beta-subunit; gene rpoB, Lactuca sativa from Ohio, USA
UniProt
beta-subunit; gene rpoB, Lycopersicon esculentum from Arkansas, USA
UniProt
beta-subunit; gene rpoB, Lycopersicon esculentum from Japan
UniProt
beta-subunit; gene rpoB, Malus domestica from Germany
UniProt
beta-subunit; gene rpoB, Malus domestica from Germany
UniProt
beta-subunit; gene rpoB, Oenothera biennis from Lithuania
UniProt
beta-subunit; gene rpoB, Oenothera biennis from Lithuania
UniProt
beta-subunit; gene rpoB, Poa pratensis from Lithuania
UniProt
beta-subunit; gene rpoB, Poa pratensis from Lithuania
UniProt
beta-subunit; gene rpoB, Prunus persica from Canada
UniProt
beta-subunit; gene rpoB, Prunus persica from Canada
UniProt
beta-subunit; gene rpoB, Spiraea sp. from New York, USA
UniProt
'Spiraea sp.' phytoplasma Spiraea stunt
beta-subunit; gene rpoB, Spiraea sp. from New York, USA
UniProt
beta-subunit; gene rpoB, Stellaria media from Lithuania
UniProt
beta-subunit; gene rpoB, Stellaria media from Lithuania
UniProt
beta-subunit; gene rpoB, Trifolium repens from Canada
UniProt
beta-subunit; gene rpoB, Trifolium repens from Canada
UniProt
'Zea mays' phytoplasma Maize bushy stunt
beta-subunit; gene rpoB, Zeamays from Mexico
UniProt
beta-subunit; gene rpoB, Malus domesticus from Germany
UniProt
beta-subunit; gene rpoB, Malus domesticus from Germany
UniProt
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643551, 643555, 677248, 692483, 694828, 701717, 703150, 703354, 703458, 703854, 704096, 704671, 705139, 705704, 705982, 721721, 722993, 723183, 723636, 738010, 738671
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the nucleotide sequence of a part, 8334 bp, of the EcoRI fish lymphocystis disease virus DNA fragment B, between the EcoRI site and 259 nucleotides downstream from the second PstI site has been deposited in GenBank accession number: L34213
SwissProt
beta-subunit; gene rpoB, Chrysanthemum coronarium from Japan
UniProt
beta-subunit; gene rpoB, Chrysanthemum coronarium from Japan
UniProt
scorpionfly, collected in June in the village of Toksovo, Leningrad region, Russia
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beta-subunit; gene rpoB, Arachis hypogaea from China
UniProt
beta-subunit; gene rpoB, Arachis hypogaea from China
UniProt
DNA-directed RNA polymerase II subunit RPB6 and subunit RPB10
R4THW7 AND R4TFI0
UniProt
Q980R2: subunit A', P58192: subunit A'', Q980R1: subunit B, P95989: subunit D, Q980A3: subunit E', Q9UXD9: subunit F, Q980L5: subunit G, Q980Q9: subunit H, Q97ZJ9: subunit K, Q980K0: subunit L, Q980Z8: subunit N, Q97ZX7: subunit P, Q980B8: subunit 13
Q980R2 and P58192 and Q980R1 and P95989 and Q980A3 and Q9UXD9 and Q980L5 and Q980Q9 and Q97ZJ9 and Q980K0 and Q980Z8 and Q97ZX7 and Q980B8
UniProt
beta-subunit; gene rpoB, Asclepias syriaca from New York, USA
UniProt
beta-subunit; gene rpoB, Asclepias syriaca from Virginia, USA
UniProt
beta-subunit; gene rpoB, Asclepias syriaca from New York, USA
UniProt
beta-subunit; gene rpoB, Asclepias syriaca from Virginia, USA
UniProt
beta-subunit; gene rpoB, Lycopersicon esculentum from Arkansas, USA
UniProt
beta-subunit; gene rpoB, Lycopersicon esculentum from Japan
UniProt
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643561, 643569, 643574, 643583, 643584, 643586, 660908, 661148, 661927, 662752, 674698, 676892, 703357, 706597
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643564, 643570, 643584, 643587, 660691, 661201, 662629, 663386, 673217, 676146, 702224, 702625, 703353, 703357, 705530, 706807, 706873, 721305, 723296
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DNA-directed RNA polymerase subunits beta, beta', and alpha encoded by genes rpoC, rpoB, and rpoA; genes rpoC, rpoB, and rpoA
P0A8T7 AND P0A8V2 AND P0A7Z4
UniProt
-
643554, 643555, 643577, 643578, 643580, 643581, 662831, 663216, 691700, 694328, 701466, 702030, 702171, 702625, 703147, 703353, 703354, 703448, 705882, 706600, 706665, 706873, 738682, 738689, 739056
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13-subunit enzyme
B8YB53 and B8YB55 and B8YB54 and B8YB56 and B8YB57 and B8YB58 and B8YB59 and B8YB60 and B8YB61 and B8YB65 and B8YB62 and B8YB63 and B8YB64
UniProt
13-subunit enzyme
B8YB53 and B8YB55 and B8YB54 and B8YB56 and B8YB57 and B8YB58 and B8YB59 and B8YB60 and B8YB61 and B8YB65 and B8YB62 and B8YB63 and B8YB64
UniProt
Q980R2: subunit A', P58192: subunit A'', Q980R1: subunit B, P95989: subunit D, Q980A3: subunit E', Q9UXD9: subunit F, Q980L5: subunit G, Q980Q9: subunit H, Q97ZJ9: subunit K, Q980K0: subunit L, Q980Z8: subunit N, Q97ZX7: subunit P, Q980B8: subunit 13
Q980R2 and P58192 and Q980R1 and P95989 and Q980A3 and Q9UXD9 and Q980L5 and Q980Q9 and Q97ZJ9 and Q980K0 and Q980Z8 and Q97ZX7 and Q980B8
UniProt
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
physiological function
additional information
evolution
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human mitochondrial RNA polymerase is distantly related to the bacteriophage T7 class of single-subunit RNAPs with a probably similar mechanisms for nucleotide binding, substrate selection and catalysis/nucleotidyl transfer. The C-terminal domain contains the regions of highest similarity to the phage RNAPs. Early in the evolution of eukaryotes there has been a switch from a multi-subunit prokaryotic polymerase to a single-subunit, phage-derived polymerase, encoded in the nuclear genome and imported into the mitochondria, to serve as the transcriptase of the mitochondrial genome. The POLRMT CTD 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
evolution
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Rpo41 utilizes a promoter recognition loop to bind and recognize its promoter, analogous to the use of the specificity loop by T7 RNAP for this purpose
evolution
Lamium sp.
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the rpo genes that encode the enzyme subunits, rpoA, rpoB, rpoC1, and rpoC2, are relatively rapidly evolving sequences. Determination of the rate of the molecular evolution of rpo genes and to evaluation as phylogenetic markers on the example of the genus Lamium, Lamiaceae, represented by 66 specimens. Distribution of substitution rates across rpo genes as calculated in HyPhy using the GTR model of evolution, overview. The process of evolution of the RNA polymerase type I enzyme in genus Lamium is due not only to the genetic drift
evolution
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview; genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
'Capsicum annum' phytoplasma
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
S5ZYX4
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
S5ZYY2
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
'Gomphocarpus physocarpus' phytoplasma
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
'Lactuca sativa' phytoplasma
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview; genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
'Zea mays' phytoplasma
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview; genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
'Capsicum annum' phytoplasma Candidatus Phytoplasma solani
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
'Gomphocarpus physocarpus' phytoplasma Candidatus Phytoplasma australiense
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
'Lactuca sativa' phytoplasma AYWB
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
'Spiraea sp.' phytoplasma Spiraea stunt
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
evolution
'Zea mays' phytoplasma Maize bushy stunt
-
genotyping and phylogenetic analysis of gene rpoB encoding the beta subunit of the DNA-directed RNA polymerase of phytoplasmas from different plant origins, detailed overview
-
malfunction
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reverse translocation, i.e. backtracking, by a distance of one or more nucleotides disrupts the configuration of the catalytic center, leading to a temporary, spontaneously resolved, halt of the RNAP, called pausing, or to a transition into an irreversible arrested state. The latter can be restored to functionality by the endonucleolytic cleavage of the RNA or by pushing the backtracked complex from behind. Non-backtracked paused complexes are also described for bacterial RNAPs, where addition of the incoming NTP is hindered owing to isomerization of the active site into an inactive conformation
malfunction
-
reverse translocation, i.e. backtracking, by a distance of one or more nucleotides disrupts the configuration of the catalytic center, leading to a temporary, spontaneously resolved, halt of the RNAP, called pausing, or to a transition into an irreversible arrested state. The latter can be restored to functionality by the endonucleolytic cleavage of the RNA or by pushing the backtracked complex from behind. Non-backtracked paused complexes are also described for bacterial RNAPs, where addition of the incoming NTP is hindered owing to isomerization of the active site into an inactive conformation
malfunction
-
reverse translocation, i.e. backtracking, by a distance of one or more nucleotides disrupts the configuration of the catalytic center, leading to a temporary, spontaneously resolved, halt of the RNAP, called pausing, or to a transition into an irreversible arrested state. The latter can be restored to functionality by the endonucleolytic cleavage of the RNA or by pushing the backtracked complex from behind. Non-backtracked paused complexes are also described for bacterial RNAPs, where addition of the incoming NTP is hindered owing to isomerization of the active site into an inactive conformation
malfunction
-
reverse translocation, i.e. backtracking, by a distance of one or more nucleotides disrupts the configuration of the catalytic center, leading to a temporary, spontaneously resolved, halt of the RNAP, called pausing, or to a transition into an irreversible arrested state. The latter can be restored to functionality by the endonucleolytic cleavage of the RNA or by pushing the backtracked complex from behind. Non-backtracked paused complexes are also described for bacterial RNAPs, where addition of the incoming NTP is hindered owing to isomerization of the active site into an inactive conformation
malfunction
-
reverse translocation, i.e. backtracking, by a distance of one or more nucleotides disrupts the configuration of the catalytic center, leading to a temporary, spontaneously resolved, halt of the RNAP, called pausing, or to a transition into an irreversible arrested state. The latter can be restored to functionality by the endonucleolytic cleavage of the RNA or by pushing the backtracked complex from behind. Non-backtracked paused complexes are also described for bacterial RNAPs, where addition of the incoming NTP is hindered owing to isomerization of the active site into an inactive conformation
malfunction
-
DNA topoisomerase I inhibition by camptothecin induces escape of RNA polymerase II from promoter-proximal pause site, antisense transcription and histone acetylation at the human HIF-1alpha gene locus
malfunction
-
at lower concentrations, pyrimidine nucleoside analogs have the potential to more easily inhibit mitochondrial transcription and mediate toxicity, given the ability to be readily phosphorylated and serve as efficient substrates for the enzyme
malfunction
-
replication intermediates associated with an unusually prolonged delay in the initiation of second strand DNA synthesis are enhanced by combined shRNA and dsRNA POLRMT gene silencing
malfunction
-
suppression of subunit RPC32alpha expression by siRNAs impedes anchorage-independent growth of HeLa cells, whereas ectopic expression of RPC32alpha in IMR90 fibroblasts enhances cell transformation and dramatically changes the expression of several tumor-related mRNAs and that of a subset of Pol III RNAs
malfunction
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rDNA silencing is attenuated by loss of Pol I subunits or insertion of an ectopic Pol I terminator within the adjacent rDNA gene. Silencing left of the rDNA array is naturally attenuated by the presence of only one intact Fob1 binding site (Ter2). Repair of the 2nd Fob1 binding site (Ter1) dramatically strengthens silencing such that it is no longer impacted by local Pol I transcription defects. Global loss of Pol I activity, negatively affects Fob1 association with the rDNA. Loss of Ter2 almost completely eliminates localized silencing, but is restored by artificially targeting Fob1 or Sir2 as Gal4 DNA binding domain fusions
malfunction
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rDNA silencing is attenuated by loss of Pol I subunits or insertion of an ectopic Pol I terminator within the adjacent rDNA gene. Silencing left of the rDNA array is naturally attenuated by the presence of only one intact Fob1 binding site (Ter2). Repair of the 2nd Fob1 binding site (Ter1) dramatically strengthens silencing such that it is no longer impacted by local Pol I transcription defects. Global loss of Pol I activity, negatively affects Fob1 association with the rDNA. Loss of Ter2 almost completely eliminates localized silencing, but is restored by artificially targeting Fob1 or Sir2 as Gal4 DNA binding domain fusions
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physiological function
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Pol II is the eukaryotic enzyme that is responsible for transcribing all protein-coding genes into mRNA. The mRNA-transcription cycle can be divided into three stages: initiation, elongation and termination. During elongation, Pol II moves along a DNA template and synthesizes a complementary RNA chain in a processive manner
physiological function
-
POLRMT is a key molecule of the core complex of the mitochondrial transcription machinery which assembles at promoter sequences on both strands of mtDNA, termed the L-strand promoter and H-strand promoter
physiological function
RNA polymerase II is the central enzyme of eukaryotic gene expression machinery, analysis of regulation mechanisms of transcription via protein-protein interactions within the Pol II apparatus, overview
physiological function
-
RNA pol III is involved in regulating the growth rate of cells
physiological function
-
RNAP is an exceptionally complex enzyme that can be thought of as the engine of gene expression
physiological function
-
RNAP is an exceptionally complex enzyme that can be thought of as the engine of gene expression
physiological function
-
RNAP-II is essential for gene expression in metazoa
physiological function
-
the enzyme from Zea mays exhibits a role in genome-wide and small RNA-associated gene silencing, but is not essential for the plant, PolIV is involved in paramutation, an inherited epigenetic change facilitated by an interaction of two alleles, overview
physiological function
-
the enzyme can be involved in both replication and integration processes of these plasmid in the mitochondrial genome
physiological function
-
RNA polymerase II has a regulatory function on nucleoside triphosphate synthesis, mutations of RNA polymerase II activate key genes of the nucleoside triphosphate biosynthetic pathways, overview
physiological function
-
the enzyme is required for expression of 13 subunits of the respiratory chain complexes involved in oxidative phosphorylation and two rRNAs and 22 tRNAs, required for mitochondrial translation. In addition to its role in transcription, in the mitochondria, POLRMT serves as the primase for mitochondrial DNA replication. Mechanisms and species specificity for promoter recognition, overview. Complex formation between the enzyme and the other transcription factors at the promoter, the structural elements of the enzyme are repositioned in such a way as to allow for specific promoter recognition, open complex formation and transcription initiation
physiological function
-
the enzyme is required for expression of 13 subunits of the respiratory chain complexes involved in oxidative phosphorylation and rRNAs and tRNAs, required for mitochondrial translation. Rpo41 can initiate transcription from negatively supercoiled templates and pre-melted promoter substrates in the absence of the yeast mitochondrial transcription factor, Mtf1. Mechanisms and species specificity for promoter recognition, overview
physiological function
-
mitochondrial DNA is replicated by a unique enzymatic machinery involving the POLRMT-mediated initiation of primer synthesis from a poly-dT stretch in the single-stranded loop region of the light-strand origin of DNA replication, when the single-stranded origin of DNA replication is exposed and adopts a stem-loop structure. The poly-dT repeat region of origin of DNA replication is an essential element for primer synthesis. POLRMT can function as an origin-specific primase in mammalian mitochondria, overview
physiological function
-
the enzyme activates genes for high affinity nutrient scavenging and motility
physiological function
-
increased Pol III transcription accompanies or causes cell transformation. RPC32beta subunit-containing isozyme Pol IIIbeta is ubiquitously expressed and essential for growth of human cells. RPC32alpha subunit-containing isozyme Pol IIIalpha is dispensable for cell survival, with expression being restricted to undifferentiated ES cells and to tumor cells. Dramatic changes in 5S RNA, U6 RNA, and 7SKRNA expression are specifically caused by ectopic expression of RPC32alpha and not due to a general deregulation of transcription
physiological function
-
RNA polymerase binds to the promoter regions of the gdh, rrnC, and rrnE genes encoding glutamate dehydrogenase and rRNA and activates their transcription
physiological function
RNA polymerase plays a crucial role in gene expression in all organisms. It is a multiprotein complex that produces primary transcript RNA from a DNA template
physiological function
Lamium sp.
-
RNA polymerase type I (plastid-encoded polymerase, PEP) is one of the key chloroplast enzymes
physiological function
P0A8T7 AND P0A8V2 AND P0A7Z4
the enzyme subunits interact with CedA, a multi-copy suppressor which represses the dnaAcos inhibition of cell division. DnaAcos is a mutant of the initiator DnaA that causes overinitiation of chromosome replication in Escherichia coli resulting in inhibition of cell division. Determination of the binding site of CedA for RNA polymerase and examination of the binding functions involved in cell division reactivation
physiological function
-
RNA polymerase III regulates the presence of cytosolic RNA:DNA hybrids and miRNA biogenesis in various human cells. RNA:DNA hybrids exist in the cytosol of various human cells and are mediated by RNA polymerase III, which regulates the microRNA machinery, cytosolic RNA:DNA hybrids may have physiological relevance to miRNA machinery and RNA transport, miRNA expression analysis, RNA transport and mRNA surveillance pathways are potential targets of Pol III-modulated miRNAs, overview. Inhibition of the DNA damage response has no effect on the presence of RNA:DNA hybrids in the cytosol, and the levels of cytosolic RNA:DNA hybrids are not modulated by genotoxic replication inhibitors
physiological function
-
the yeast mitochondrial RNA polymerase and transcription factor complex catalyzes efficient priming of DNA synthesis on single-stranded DNA. Primases are specialized DNA-dependent RNA polymerases that synthesize short oligoribonucleotides de novo on single-stranded (ss) DNA templates
physiological function
-
basal transcriptional activity and RNAPII DNA binding might be associated with the O-GlcNAcylation and/or phosphorylation state of RNAPII, which can involve changed association with other transcription factors during inflammation
physiological function
-
binding of the termination factor Nsi1 to its cognate DNA site is sufficient to terminate RNA polymerase I transcription in vitro and to induce termination in vivo. Nsi1 contains Myb-like DNA binding domains and associates in vivo near the 3' end of rRNA genes to rDNA
physiological function
-
active Pol I transcription is critical for silencing of Pol II transcription within the rDNA. Sir2 is recruited to the rDNA promoter through interactions with RNA polymerase I, Sir2 suppresses RNA polymerase II (Pol II)-transcribed genes embedded within the yeast rDNA locus, i.e. rDNA silencing. Fob1 and Pol Imake independent contributions to establishment of silencing, though Pol I also reinforces Fob1-dependent silencing
physiological function
plastid genes are transcribed by two types of RNA polymerases: a plastid-encoded eubacterial-type RNA polymerase and nuclear-encoded phage-type RNA polymerases, spatio-temporal expression of plastid RNA polymerase. The association of plastid RNA polymerase with photosynthesis-related genes is reduced during the dark period, indicating that plastome-wide plastid RNA polymerase-DNA association is a light-dependent process
physiological function
-
active Pol I transcription is critical for silencing of Pol II transcription within the rDNA. Sir2 is recruited to the rDNA promoter through interactions with RNA polymerase I, Sir2 suppresses RNA polymerase II (Pol II)-transcribed genes embedded within the yeast rDNA locus, i.e. rDNA silencing. Fob1 and Pol Imake independent contributions to establishment of silencing, though Pol I also reinforces Fob1-dependent silencing
-
physiological function
-
binding of the termination factor Nsi1 to its cognate DNA site is sufficient to terminate RNA polymerase I transcription in vitro and to induce termination in vivo. Nsi1 contains Myb-like DNA binding domains and associates in vivo near the 3' end of rRNA genes to rDNA
-
additional information
-
structure-based analysis of the evolution of archaeal and eukaryotic DNA-dependent RNA polymerases, overview
additional information
-
structure-based analysis of the evolution of archaeal and eukaryotic DNA-dependent RNA polymerases, overview
additional information
-
structure-based analysis of the evolution of archaeal and eukaryotic DNA-dependent RNA polymerases, overview
additional information
-
structure-based analysis of the evolution of archaeal and eukaryotic DNA-dependent RNA polymerases, overview
additional information
-
structure-based analysis of the evolution of archaeal and eukaryotic DNA-dependent RNA polymerases, overview
additional information
-
structure-based analysis of the evolution of archaeal and eukaryotic DNA-dependent RNA polymerases, overview
additional information
-
structure-based analysis of the evolution of archaeal and eukaryotic DNA-dependent RNA polymerases, overview
additional information
-
structure-based analysis of the evolution of archaeal and eukaryotic DNA-dependent RNA polymerases, overview
additional information
-
structure-based analysis of the evolution of archaeal and eukaryotic DNA-dependent RNA polymerases, overview
additional information
-
structure-based analysis of the evolution of archaeal and eukaryotic DNA-dependent RNA polymerases, overview
additional information
-
in vitro assembly of Sc RNAP II ternary elongation complexes, overview. RNA polymerase in a catalytic conformation demonstrates that the active site dNMP-NTP base pair must be substantially dehydrated to support full active site closing and optimum conditions for phosphodiester bond synthesis. An active site latch assembly that includes a key trigger helix residue beta' H1242 and highly conserved active site residues beta E445 and R557 appears to help regulate active site hydration/dehydration. Molecular dynamics simulations, overview
additional information
-
modeling of Tt RNAP TEC containing a closed, catalytic trigger helix conformation. RNA polymerase in a catalytic conformation demonstrates that the active site dNMP-NTP base pair must be substantially dehydrated to support full active site closing and optimum conditions for phosphodiester bond synthesis. An active site latch assembly that includes a key trigger helix residue beta' H1242 and highly conserved active site residues beta E445 and R557 appears to help regulate active site hydration/dehydration. Molecular dynamics simulations, overview
additional information
-
POLRMT distinct mechanisms for promoter recognition and transcription initiation, kinetic mechanism for POLRMT-catalyzed nucleotide incorporation, and structure-function relationship, nucleotidyl transfer and the nucleotide-addition cycle, detailed overview
additional information
Q5UQ32 AND E3VZD2
DNA-dependent RNA polymerase (RNAP) genes are universal in microbes and conserved in giant viruses and may replace rDNA for identifying microbes
additional information
R4THW7 AND R4TFI0
DNA-dependent RNA polymerase (RNAP) genes are universal in microbes and conserved in giant viruses and may replace rDNA for identifying microbes
additional information
-
DNA-dependent RNA polymerase (RNAP) genes are universal in microbes and conserved in giant viruses and may replace rDNA for identifying microbes
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2'-C-methyl-ATP + RNAn
diphosphate + RNAn+1
-
misincorporation frequency of approximately 1 in 7800 2'-C-methyl-ATP
-
-
?
3'-deoxy-ATP + RNAn
diphosphate + RNAn+1
-
misincorporation frequency of approximately 1 in 5 3'-dATP
-
-
?
nucleoside triphosphate + A10G2A2C2C
?
-
oligonucleotide extension
-
-
?
nucleoside triphosphate + A9G3A2C2C
?
-
oligonucleotide extension
-
-
?
nucleoside triphosphate + G2CAC2C
?
-
oligonucleotide extension
-
-
?
nucleoside triphosphate + T10G2T2C2C
?
-
oligonucleotide extension
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
Autographa californica M nucleopolyhedrovirus
-
Autographa californica M nucleopolyhedrovirus transcribes genes using two DNA-directed RNA polymerases. Early genes are transcribed by the host RNA polymerase II, and late and very late genes are transcribed by a viral-encoded multisubunit RNA polymerase
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
RNAP is an exceptionally complex enzyme that can be thought of as the engine of gene expression, synthesis of RNA transcripts of many thousands of nucleotides without dissociation. Energy, in the form of nucleoside triphosphates, fuels the synthesis of an RNA polymer complementary to specific regions of the DNA template. Like all macromolecular synthesis, RNA synthesis can be divided into three general phases: initiation, elongation, and termination. Importantly, each of these phases can be a target of regulation. Promoter recognition, binding at the extended promoter recognition region, and transcript initiation, RNAP prefers to initiate transcription within a narrow window located between 6 and 9 bp downstream of the -10 element, promoter clearance and elongation, termination and recycling, mechanisms and regulation , overview. The process of start site selection can be governed by the availability of either the +1 or the +2 NTP, depending on the promoter
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
absolutely dependent on the presence of a double-stranded or single-stranded DNA template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
with poly(dA-dT) DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
denatured calf-thymus DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
transcription elongation as a critical regulatory step in addition to initiation
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
DNA-template dependent reaction. T7 DNA and the plasmid PBR322 are by far the best templates. P2, T4 and T5 DNA are weak templates
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
DNA-template dependent reaction. T7 DNA and the plasmid PBR322 are by far the best templates. P2, T4 and T5 DNA are weak templates
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the catalytic specificity for ribonucleoside triphosphates vs. deoxynucleoside triphosphates during transcript elongation is 80
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
mediates fast promoter-independent extension of unstable nucleic acid complexes
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
short DNA or RNA substrates are good substrates for the enzyme
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
substrate specifically binds to the enzyme in the open conformation, where it is base paired with the acceptor template base, while Tyr639 provides discrimination of ribose versus deoxyribose substrates. Substrate selection occurs prior to the isomerization to the catalytically active conformation
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the single subunit DNA-dependent RNA polymerase from bacteriophage T7 catalyzes both promoterdependent transcription initiation and promoter-independent elongation
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
mechanism for de novo RNA synthesis, transcription begins with a marked preference for GTP at the +1 and +2 positions
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
T7 RNAP undergoes a slow conformational change to form an elongation competent complex with the promoter-free substrate. The complex binds to a correct NTP and incorporates the nucleoside monophosphate into RNA primer very efficiently. In the presence of inorganic pyrophosphate, the elongation complex catalyzes the reverse pyrophosphorolysis reaction at a maximum rate of 0.8 per s
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
two proton transfer occurs in the transition state for nucleotidyl-transfer reaction. Associative-like transition-state structure
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
a kind of transcription complex is formed during RNA polymerase catalysed synthesis of the M13 bacteriophage replication primer. The complex contains an overextended RNADNA hybrid bound in the RNA-polymerase through that is normally occupied by downstream double-stranded DNA, thus leaving the 30 end of the RNA available for interaction with DNA polymerase
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
enzyme is responsible for transcription in bacteria
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
regulation by anions, overview
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
RNAP is an exceptionally complex enzyme that can be thought of as the engine of gene expression, synthesis of RNA transcripts of many thousands of nucleotides without dissociation. Energy, in the form of nucleoside triphosphates, fuels the synthesis of an RNA polymer complementary to specific regions of the DNA template. Like all macromolecular synthesis, RNA synthesis can be divided into three general phases: initiation, elongation, and termination. Importantly, each of these phases can be a target of regulation. Promoter recognition, binding at the extended promoter recognition region, and transcript initiation, RNAP prefers to initiate transcription within a narrow window located between 6 and 9 bp downstream of the -10 element, promoter clearance and elongation, termination and recycling, mechanisms and regulation , overview. The process of start site selection can be governed by the availability of either the +1 or the +2 NTP, depending on the promoter
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA, native or denatured, method evaluation: specificity and extent of transcription depends strongly on the quality of the DNA preparation, the strength of the promoter and terminator sequences, and the kind and concentration of mono- and divalent cations in the reaction mixture
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is supercoiled DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
minimal M13 origin hairpin is bound in the RNAP core channel normally occupied by dsDNA downstream of the transcription initiation start site, the sigma subunit is not required for initiation of RNA synthesis but it is essential for escape into productive elongation, RNAP recognition of the M13 ori and mechanism of RNA synthesis during transcription, detailed overview. During transcription elongation, RNAP can processively synthesize RNAs for thousands of nt. Mechanism of priming on dsDNA, overview
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
-
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the hepatitis delta virus is an RNA virus that depends on DNA-dependent RNA polymerase for its transcription and replication. The association between human RNAP II and hepatitis delta virus RNA suggest two transcription start sites on both polarities of hepatitis delta virus RNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
RNAPIIis recruited to gene promoters in a hypo-phosphorylated state
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA, epigenetic control of rDNA transcription, regulation system of RNA polymerase, detailed overview
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
DNA supercoiling-dependent and LSP-dependent RNA synthesis, three templates are used for in vitro RNA synthesis: the run-off template contains the light strand promoter, conserved sequence blocks, and heavy-strand origin. Promoter-independent RNA synthesis is dependent on DNA supercoiling and on TFB2M
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
in vitro transcription reactions with ATP, CTP, 3'-methyl-GTP, UTP, and DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
-
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
Leishmania sp. UR6
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA, epigenetic control of rDNA transcription, regulation system of RNA polymerase, detailed overview
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
in vitro transcription with calf thymus DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
Mycobacterium smegmatis mc(2)155 / ATCC 700084
-
in vitro transcription with calf thymus DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
DNA-directed RNA polymerase activity
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
supercoiled, double-stranded DNA template is more efficient than that from nonsupercoiled DNA, in vitro transcription activity and mechanism, overview
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme is able to use a variety of DNA templates. DNA from bacteriphage phiPLS27 is transcribed more efficiently than DNA isolated from lamda or herring sperm. DNA isolated from bacteriophage T7 and T7 D111 is utilized more efficiently
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
recruitment of the enzyme is a rate-limiting step for the activation of the sigma(54) promoter Pu of Pseudomonas putida, overview
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
in vitro transcription reactions with ATP, CTP, GTP, UTP, and oligo(dC)-tailed DNA template derived from pAd-GR220
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
-
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA, RNA translation process and mechanism of DNA-damage recognition by Pol II, detailed overview
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is plasmid DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
Rpo41 and Rpo41-Mtf1 synthesize RNA on M13 ssDNA template
30-nt and 41-nt products of Rpo41 and 30-nt, 41-nt, and 60-nt products of Rpo41-Mtf1
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
DNA-template dependent reaction. The best of the templates is phiH DNA, whereas T7 and T4 DNA are comparatively inactive and P2 DNA is a very weak template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
DNA-template dependent reaction. The best of the templates is phiH DNA, whereas T7 and T4 DNA are comparatively inactive and P2 DNA is a very weak template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
-
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
Q980R2 and P58192 and Q980R1 and P95989 and Q980A3 and Q9UXD9 and Q980L5 and Q980Q9 and Q97ZJ9 and Q980K0 and Q980Z8 and Q97ZX7 and Q980B8
-
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
Q980R2 and P58192 and Q980R1 and P95989 and Q980A3 and Q9UXD9 and Q980L5 and Q980Q9 and Q97ZJ9 and Q980K0 and Q980Z8 and Q97ZX7 and Q980B8
-
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
DNA-template dependent reaction. The enzyme transcribes phiH DNA as efficiently and T4 DNA as weakly as the Sulfolobus enzyme but T7 DNA even better than phiH DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
DNA-template dependent reaction. The enzyme transcribes phiH DNA as efficiently and T4 DNA as weakly as the Sulfolobus enzyme but T7 DNA even better than phiH DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme is highly active with poly dAT or T7 phage DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme can bind to DNA containing the lambdaPR promoter, form an open complex and initiate transcription in a temperature-dependent manner. The organism relies on the high temperature of its environment to provide the thermal energy required to stimulate open promoter complex formation, initiate transcription, and facilitate the conformational changes in RNA polymerase that results in nucleotide incorporation
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
calf thymus DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
calf thymus DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
the enzyme can bind to DNA containing the lambdaPR promoter, form an open complex and initiate transcription in a temperature-dependent manner. The organism relies on the high temperature of its environment to provide the thermal energy required to stimulate open promoter complex formation, initiate transcription, and facilitate the conformational changes in RNA polymerase that results in nucleotide incorporation
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
higher error ratios in transcription by RNA polymerase II are observed in the presence of Mn2+ compared to Mg2+. RNA polymerase II is able to elongate a primer with a 3'-terminal mismatch and thus to incorporate the mismatched nucleotide stable in the nascent RNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
nucleoside triphosphate phosphohydrolase I binds to the H4L subunit of virion RNA polymerase. These observation provides an explanation that UUUUUNU-dependent transcription termination is restricted to early genes, whose transcription is catalyzed by the H4L-containing virion RNA polymerase
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
nucleoside triphosphate phosphohydrolase I binds to the H4L subunit of virion RNA polymerase. These observation provides an explanation that UUUUUNU-dependent transcription termination is restricted to early genes, whose transcription is catalyzed by the H4L-containing virion RNA polymerase
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
additional information
?
-
-
dinucleoside teraphosphates are more potent substrates than dinucleoside triphosphates and dinucleoside pentaphosphates
-
-
-
additional information
?
-
-
multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions
-
-
-
additional information
?
-
-
RNAP adds nucleotides to the 3'-end of the growing RNA and translocates reiteratively, in single nucleotide steps. Translocation mechanism models, concerning conformational changes, allosteric effects and isomerization, and model evaluation, overview
-
-
-
additional information
?
-
-
the core enzyme, which lacks the sigma subunit, synthesizes short transcripts relatively uniformly on the DNA template in the presence of high concentrations of random primers and low NTP concentrations
-
-
-
additional information
?
-
-
dsDNA templates used for activity are T7A1_763, T7A1_437, T7A1_149, pcDNA3.1, pGEM, T-phage DNA, Escherichia coli DNA, calf thymus DNA, poly(dA-dT), and Kool NC-45
-
-
-
additional information
?
-
-
RNA polymerase binds multiple sites in the ehxCABD gene regulatory region. At the Escherichia coli ehxCABD operon, RNA polymerase is unable to distinguish between the promoter -10 element and similar overlapping sequences. RNA polymerase competes with itself for binding to AT-rich sequences overlapping PehxCABD, correct positioning of RNA polymerase at PehxCABD requires H-NS
-
-
-
additional information
?
-
P0A8T7 AND P0A8V2 AND P0A7Z4
the subunits interact with recombinant His6-tagged CedA, a multi-copy suppressor which represses the dnaAcos inhibition of cell division. Determination of the binding site of CedA for RNA polymerase. The N-terminus of CedA is necessary for a tight interaction
-
-
-
additional information
?
-
-
multisubunit RNA polymerase transcribes DNA, but is also known to synthesize DNA replication primers in the replication system, a function that is commonly performed by primases, mechanism of primer synthesis by RNA polymerase and comparison to the mechanism of both types of primases, overview
-
-
-
additional information
?
-
-
molecular mechanisms of transcription regulation in mitochondria, molecular organization of the human mitochondrial transcription initiation complex, overview
-
-
-
additional information
?
-
-
RNA pol III transcribes structural RNAs involved in RNA processing, U6 snRNA, and translation, tRNA. Mechanism of regulation of RNA pol III transcription by BRCA1, overview
-
-
-
additional information
?
-
-
RNA polymerase II phosphorylation during paused, active and poised transcription cycles with in itiation and elongation stages and at different phosphorylation stages, RNA polymerase II and histone modification profiles across genes in paused, active and poised states, and RNAPII regulation mechanisms at active genes, detailed overview. In embryonic stem cells, silent developmental regulator genes that are repressed by Polycomb are associated with a form of RNAPII that can elongate through coding regions but that lacks the post-translational modifications that are important for coupling RNA synthesis to co-transcriptional maturation
-
-
-
additional information
?
-
-
TLS regulates both RNAPs II and III and supports the possibility that cross-regulation between RNA polymerases is important in maintaining normal cell growth
-
-
-
additional information
?
-
-
two distinct forms, Pol Ialpha and Pol Ibeta. Both forms are catalytically active, but only Pol Ibeta can assemble into productive transcription initiation complexes. Regulation of Pol I transcription during cell cycle progression involving cytokines, and structural organization of mammalian rDNA repeats and the basal factors required for transcription initiation, overview. The activity of basal Pol I factors is regulated by posttranslational modifications
-
-
-
additional information
?
-
-
negative DNA supercoiling favors the induction of unpaired regions at some sequence motifs on dsDNA, substrate specificity and structural effects on activity, overview
-
-
-
additional information
?
-
-
RNA polymerase III transcribes small untranslated RNAs that include tRNAs, 5S RNA, U6 RNA, and some microRNAs
-
-
-
additional information
?
-
-
the B2 family of short interspersed elements is transcribed into non-coding RNA by RNA polymerase III
-
-
-
additional information
?
-
-
POLRMT can act as a primase in vitro and support lagging-strand DNA synthesis on a small 70 bp minicircle, overview
-
-
-
additional information
?
-
-
RNAP II participates in the generation of mRNAs and most of the small nuclear RNAs, while RNAP III synthesizes small essential RNAs, such as tRNAs, 5S rRNA and some snRNAs
-
-
-
additional information
?
-
-
RNAP II participates in the generation of mRNAs and most of the small nuclear RNAs, while RNAP III synthesizes small essential RNAs, such as tRNAs, 5S rRNA and some snRNAs
-
-
-
additional information
?
-
-
active site structure formed by amino acids from two domains: Palm with Asp457 and Asp695, and Fingers with Tyr537 and Lys529, overview
-
-
-
additional information
?
-
-
intermittent hypoxia, a major pathological factor in the development of neural deficits associated with sleep-disordered breathing, regulates RNA polymerase II in hippocampus and prefrontal cortex. Chronic intermittent hypoxia, but not sustained hypoxia, stimulates hydroxylation of Pro1465 in large subunit of RNA polymerase II and phosphorylation of Ser5 of Rpb1, specifically in the CA1 region of the hippocampus and in the prefrontal cortex but not in other regions of the brain, requiring the von Hippel-Lindau tumor suppressor. Mice exposed to chronic IH demonstrated cognitive deficits related to dysfunction in those brain regions, overview
-
-
-
additional information
?
-
-
two distinct forms, Pol Ialpha and Pol Ibeta. Both forms are catalytically active, but only Pol Ibeta can assemble into productive transcription initiation complexes. Regulation of Pol I transcription during cell cycle progression involving cytokines, and structural organization of mammalian rDNA repeats and the basal factors required for transcription initiation, overview. The activity of basal Pol I factors is regulated by posttranslational modifications
-
-
-
additional information
?
-
-
the RNAP purified from exponential phase shows low promoter specificity in promoter-polymerase interaction studies due to the presence of a large number of sigma factors during exponential phase and under-representation of sigma A required for house-keeping transcription
-
-
-
additional information
?
-
Mycobacterium smegmatis mc(2)155 / ATCC 700084
-
the RNAP purified from exponential phase shows low promoter specificity in promoter-polymerase interaction studies due to the presence of a large number of sigma factors during exponential phase and under-representation of sigma A required for house-keeping transcription
-
-
-
additional information
?
-
-
the two rpoB paralogues, rpoB(S) and rpoB(R), are two functionally distinct and developmentally regulated RNA polymerases, overview. A five amino acid substitutions located within or close to the so-called rifampin resistance clusters of rpoB(R) plays a key role in fundamental activities of the RNA polymerase. The rpoB(R)-specific missense mutation H426N is essential for the activation of secondary metabolism, molecular mechanism, overview
-
-
-
additional information
?
-
-
identification of an activity associated with the mtRNAP in which non-DNA-templated nucleotides are added to the 3' end of RNAs, any of the four rNTPs can act as precursors for this process, RNA editing mechanism, overview. Nucleotides that are not specified by the mitochondrial DNA templates are inserted into some RNAs, a process called RNA editing. This is an essential step in the expression of these RNAs, as the insertion of the nontemplated nucleotides creates open reading frames for the production of proteins from mRNAs or produces required secondary structure in rRNAs and tRNAs
-
-
-
additional information
?
-
-
bacterial anti-sigma factors typically regulate sigma factor function by restricting the access of their cognate sigma-factors to the RNA polymerase RNAP core enzyme, regulation of RNAP holoenzyme, Esigma70, involving Rsd and the Rsd orthologue AlgQ, a global regulator of gene expression in Pseudomonas aeruginosa, which simultaneously interact with conserved region 2 and region 4 of sigma70 mediated by separate surfaces of Rsd, interaction with mutants of Rsd and AlgQ, mechanism, detailed overview. Rsd can strongly regulate the production of the Pseudomonas aeruginosa virulence factor pyocyanin in a manner that depends on their abilities to interact with sigma70 region 2
-
-
-
additional information
?
-
-
molecular mechanisms enabling sigma factor PvdS, directing the transcription of pyoverdine and virulence genes under iron limitation, to compete with the major sigma RpoD for RNA polymerase binding, overview
-
-
-
additional information
?
-
-
multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions
-
-
-
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, overview
-
-
-
additional information
?
-
-
RNAP function through the transcription cycle with initiation/re-initiation, elongation, and termination, detailed overview
-
-
-
additional information
?
-
-
RNAPII recruits COMPASS, a histone methyltransferase, as well as the regulator Paf1C, to the transcription active site causing methylation of histone H3K4 in a transcription-dependent manner. The large RNAPII subunit Rpb1 attracts FACT, a transcription factor that FACT participates in regulation of DNA repair and replication, to the transcription site, and Rpb1 also interacts with RSC, an abundant Swi/Snf-like chromatin remodeling complex with multiple subunits, and other general transcription factors, as well as with histone chaperone proteins, mRNA processing and export factors, DNA repair factors, protein kinases, and other cellular proteins, overview
-
-
-
additional information
?
-
-
the phosphatase activity of Cdc14 is required for Pol I inhibition, transcription inhibition is necessary for complete chromosome disjunction, because rRNA transcripts block condensin binding to rDNA, and show that bypassing the role of Cdc14 in nucleolar segregation requires in vivo degradation of nascent transcripts, transcription interferes with chromosome condensation, not the reverse
-
-
-
additional information
?
-
-
the Switch 1 loop of RNA polymerase II, located at the downstream end of the transcription bubble, may operate as a specific sensor of the nucleoside triphosphates available for transcription. Regulatory effects of RNA polymerase II on URA2 gene, encoding the rate-limiting enzyme of UTP biosynthesis after activation by UTP shortage, RNA polymerase II occupancy is increased on the URA2 open reading frame, overview
-
-
-
additional information
?
-
-
RNAP adds nucleotides to the 3'-end of the growing RNA and translocates reiteratively, in single nucleotide steps. Translocation mechanism models, concerning conformational changes, allosteric effects and isomerization, and model evaluation, overview
-
-
-
additional information
?
-
-
the enzyme also shows RNA-dependent RNA polymerase activity, EC 2.7.7.48, but slower and less processive than the DNA-dependent activity. During active transcription, Pol II must overcome intrinsic DNA-arrest sites, which are generally rich in A-T base pairs and pose a natural obstacle to transcription. At such sites, Pol II moves backwards along DNA and RNA, resulting in extrusion of the RNA 3' end through the polymerase pore beneath the active site and transcriptional arrest. The RNA cleavage stimulatory factor TFIIS can rescue an arrested polymerase by creating a new RNA 3' end at the active site from which transcription can resume, mechanism, overview
-
-
-
additional information
?
-
-
mitochondrial RNA polymerase (Rpo41) and its transcription factor (Mtf1) are an efficient primase that initiates DNA synthesis on ssDNA coated with the yeast mitochondrial ssDNA-binding protein, Rim1. Both Rpo41 and Rpo41-Mtf1 can synthesize short and long RNAs on ssDNA template and prime DNA synthesis by the yeast mitochondrial DNA polymerase Mip1. Regarding the RNA-DNA products, Rpo41 and Rpo41-Mtf1 have slightly different priming specificity. Both prefer to initiate with ATP from short priming sequences such as 3'-TCC, TTC, and TTT, and the consensus sequence is 3'-Pu(Py)2-3
-
-
-
additional information
?
-
-
quantitative reverse transcriptase-PCR expression analysis
-
-
-
additional information
?
-
-
quantitative reverse transcriptase-PCR expression analysis
-
-
-
additional information
?
-
-
determination of the substrate binding site
-
-
-
additional information
?
-
-
multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions
-
-
-
additional information
?
-
-
RNAP function through the transcription cycle with initiation/re-initiation, elongation, and termination, detailed overview
-
-
-
additional information
?
-
-
RNAP adds nucleotides to the 3'-end of the growing RNA and translocates reiteratively, in single nucleotide steps. Translocation mechanism models, concerning conformational changes, allosteric effects and isomerization, and model evaluation, overview
-
-
-
additional information
?
-
-
the enzyme active site is located on the back wall of the channel, where an essential Mg2+ ion is chelated by three Asp of the absolutely conserved NADFDGD motif in the A' subunit
-
-
-
additional information
?
-
-
multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions
-
-
-
additional information
?
-
-
RNAP function through the transcription cycle with initiation/re-initiation, elongation, and termination, detailed overview
-
-
-
additional information
?
-
-
RNAP adds nucleotides to the 3'-end of the growing RNA and translocates reiteratively, in single nucleotide steps. Translocation mechanism models, concerning conformational changes, allosteric effects and isomerization, and model evaluation, overview
-
-
-
additional information
?
-
-
multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions
-
-
-
additional information
?
-
-
RNAP adds nucleotides to the 3'-end of the growing RNA and translocates reiteratively, in single nucleotide steps. Translocation mechanism models, concerning conformational changes, allosteric effects and isomerization, and model evaluation, overview
-
-
-
additional information
?
-
-
the RNAP clamp head domain constitutes the wall of the main channel opposite the catalytic centre and forms crucial contacts with the DNA template strand in the elongation complex
-
-
-
additional information
?
-
-
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
-
-
-
additional information
?
-
in vitro transcriptional activity of recombinant assembled Xcc RNAP, overview
-
-
-
additional information
?
-
in vitro transcriptional activity of recombinant assembled Xcc RNAP, overview
-
-
-
additional information
?
-
in vitro transcriptional activity of recombinant assembled Xcc RNAP, overview
-
-
-
additional information
?
-
in vitro transcriptional activity of recombinant assembled Xcc RNAP, overview
-
-
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
Autographa californica M nucleopolyhedrovirus
-
Autographa californica M nucleopolyhedrovirus transcribes genes using two DNA-directed RNA polymerases. Early genes are transcribed by the host RNA polymerase II, and late and very late genes are transcribed by a viral-encoded multisubunit RNA polymerase
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
RNAP is an exceptionally complex enzyme that can be thought of as the engine of gene expression, synthesis of RNA transcripts of many thousands of nucleotides without dissociation. Energy, in the form of nucleoside triphosphates, fuels the synthesis of an RNA polymer complementary to specific regions of the DNA template. Like all macromolecular synthesis, RNA synthesis can be divided into three general phases: initiation, elongation, and termination. Importantly, each of these phases can be a target of regulation. Promoter recognition, binding at the extended promoter recognition region, and transcript initiation, RNAP prefers to initiate transcription within a narrow window located between 6 and 9 bp downstream of the -10 element, promoter clearance and elongation, termination and recycling, mechanisms and regulation , overview. The process of start site selection can be governed by the availability of either the +1 or the +2 NTP, depending on the promoter
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
transcription elongation as a critical regulatory step in addition to initiation
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
mediates fast promoter-independent extension of unstable nucleic acid complexes
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the single subunit DNA-dependent RNA polymerase from bacteriophage T7 catalyzes both promoterdependent transcription initiation and promoter-independent elongation
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
a kind of transcription complex is formed during RNA polymerase catalysed synthesis of the M13 bacteriophage replication primer. The complex contains an overextended RNADNA hybrid bound in the RNA-polymerase through that is normally occupied by downstream double-stranded DNA, thus leaving the 30 end of the RNA available for interaction with DNA polymerase
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
enzyme is responsible for transcription in bacteria
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
regulation by anions, overview
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
RNAP is an exceptionally complex enzyme that can be thought of as the engine of gene expression, synthesis of RNA transcripts of many thousands of nucleotides without dissociation. Energy, in the form of nucleoside triphosphates, fuels the synthesis of an RNA polymer complementary to specific regions of the DNA template. Like all macromolecular synthesis, RNA synthesis can be divided into three general phases: initiation, elongation, and termination. Importantly, each of these phases can be a target of regulation. Promoter recognition, binding at the extended promoter recognition region, and transcript initiation, RNAP prefers to initiate transcription within a narrow window located between 6 and 9 bp downstream of the -10 element, promoter clearance and elongation, termination and recycling, mechanisms and regulation , overview. The process of start site selection can be governed by the availability of either the +1 or the +2 NTP, depending on the promoter
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
minimal M13 origin hairpin is bound in the RNAP core channel normally occupied by dsDNA downstream of the transcription initiation start site, the sigma subunit is not required for initiation of RNA synthesis but it is essential for escape into productive elongation, RNAP recognition of the M13 ori and mechanism of RNA synthesis during transcription, detailed overview. During transcription elongation, RNAP can processively synthesize RNAs for thousands of nt. Mechanism of priming on dsDNA, overview
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
-
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the hepatitis delta virus is an RNA virus that depends on DNA-dependent RNA polymerase for its transcription and replication. The association between human RNAP II and hepatitis delta virus RNA suggest two transcription start sites on both polarities of hepatitis delta virus RNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
RNAPIIis recruited to gene promoters in a hypo-phosphorylated state
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA, epigenetic control of rDNA transcription, regulation system of RNA polymerase, detailed overview
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA, epigenetic control of rDNA transcription, regulation system of RNA polymerase, detailed overview
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
recruitment of the enzyme is a rate-limiting step for the activation of the sigma(54) promoter Pu of Pseudomonas putida, overview
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
-
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
-
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
Q980R2 and P58192 and Q980R1 and P95989 and Q980A3 and Q9UXD9 and Q980L5 and Q980Q9 and Q97ZJ9 and Q980K0 and Q980Z8 and Q97ZX7 and Q980B8
-
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
Q980R2 and P58192 and Q980R1 and P95989 and Q980A3 and Q9UXD9 and Q980L5 and Q980Q9 and Q97ZJ9 and Q980K0 and Q980Z8 and Q97ZX7 and Q980B8
-
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme can bind to DNA containing the lambdaPR promoter, form an open complex and initiate transcription in a temperature-dependent manner. The organism relies on the high temperature of its environment to provide the thermal energy required to stimulate open promoter complex formation, initiate transcription, and facilitate the conformational changes in RNA polymerase that results in nucleotide incorporation
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
the enzyme can bind to DNA containing the lambdaPR promoter, form an open complex and initiate transcription in a temperature-dependent manner. The organism relies on the high temperature of its environment to provide the thermal energy required to stimulate open promoter complex formation, initiate transcription, and facilitate the conformational changes in RNA polymerase that results in nucleotide incorporation
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
nucleoside triphosphate phosphohydrolase I binds to the H4L subunit of virion RNA polymerase. These observation provides an explanation that UUUUUNU-dependent transcription termination is restricted to early genes, whose transcription is catalyzed by the H4L-containing virion RNA polymerase
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
nucleoside triphosphate phosphohydrolase I binds to the H4L subunit of virion RNA polymerase. These observation provides an explanation that UUUUUNU-dependent transcription termination is restricted to early genes, whose transcription is catalyzed by the H4L-containing virion RNA polymerase
-
-
?
additional information
?
-
-
multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions
-
-
-
additional information
?
-
-
RNA polymerase binds multiple sites in the ehxCABD gene regulatory region. At the Escherichia coli ehxCABD operon, RNA polymerase is unable to distinguish between the promoter -10 element and similar overlapping sequences. RNA polymerase competes with itself for binding to AT-rich sequences overlapping PehxCABD, correct positioning of RNA polymerase at PehxCABD requires H-NS
-
-
-
additional information
?
-
-
multisubunit RNA polymerase transcribes DNA, but is also known to synthesize DNA replication primers in the replication system, a function that is commonly performed by primases, mechanism of primer synthesis by RNA polymerase and comparison to the mechanism of both types of primases, overview
-
-
-
additional information
?
-
-
molecular mechanisms of transcription regulation in mitochondria, molecular organization of the human mitochondrial transcription initiation complex, overview
-
-
-
additional information
?
-
-
RNA pol III transcribes structural RNAs involved in RNA processing, U6 snRNA, and translation, tRNA. Mechanism of regulation of RNA pol III transcription by BRCA1, overview
-
-
-
additional information
?
-
-
RNA polymerase II phosphorylation during paused, active and poised transcription cycles with in itiation and elongation stages and at different phosphorylation stages, RNA polymerase II and histone modification profiles across genes in paused, active and poised states, and RNAPII regulation mechanisms at active genes, detailed overview. In embryonic stem cells, silent developmental regulator genes that are repressed by Polycomb are associated with a form of RNAPII that can elongate through coding regions but that lacks the post-translational modifications that are important for coupling RNA synthesis to co-transcriptional maturation
-
-
-
additional information
?
-
-
TLS regulates both RNAPs II and III and supports the possibility that cross-regulation between RNA polymerases is important in maintaining normal cell growth
-
-
-
additional information
?
-
-
two distinct forms, Pol Ialpha and Pol Ibeta. Both forms are catalytically active, but only Pol Ibeta can assemble into productive transcription initiation complexes. Regulation of Pol I transcription during cell cycle progression involving cytokines, and structural organization of mammalian rDNA repeats and the basal factors required for transcription initiation, overview. The activity of basal Pol I factors is regulated by posttranslational modifications
-
-
-
additional information
?
-
-
RNA polymerase III transcribes small untranslated RNAs that include tRNAs, 5S RNA, U6 RNA, and some microRNAs
-
-
-
additional information
?
-
-
the B2 family of short interspersed elements is transcribed into non-coding RNA by RNA polymerase III
-
-
-
additional information
?
-
-
RNAP II participates in the generation of mRNAs and most of the small nuclear RNAs, while RNAP III synthesizes small essential RNAs, such as tRNAs, 5S rRNA and some snRNAs
-
-
-
additional information
?
-
-
RNAP II participates in the generation of mRNAs and most of the small nuclear RNAs, while RNAP III synthesizes small essential RNAs, such as tRNAs, 5S rRNA and some snRNAs
-
-
-
additional information
?
-
-
intermittent hypoxia, a major pathological factor in the development of neural deficits associated with sleep-disordered breathing, regulates RNA polymerase II in hippocampus and prefrontal cortex. Chronic intermittent hypoxia, but not sustained hypoxia, stimulates hydroxylation of Pro1465 in large subunit of RNA polymerase II and phosphorylation of Ser5 of Rpb1, specifically in the CA1 region of the hippocampus and in the prefrontal cortex but not in other regions of the brain, requiring the von Hippel-Lindau tumor suppressor. Mice exposed to chronic IH demonstrated cognitive deficits related to dysfunction in those brain regions, overview
-
-
-
additional information
?
-
-
two distinct forms, Pol Ialpha and Pol Ibeta. Both forms are catalytically active, but only Pol Ibeta can assemble into productive transcription initiation complexes. Regulation of Pol I transcription during cell cycle progression involving cytokines, and structural organization of mammalian rDNA repeats and the basal factors required for transcription initiation, overview. The activity of basal Pol I factors is regulated by posttranslational modifications
-
-
-
additional information
?
-
-
the two rpoB paralogues, rpoB(S) and rpoB(R), are two functionally distinct and developmentally regulated RNA polymerases, overview. A five amino acid substitutions located within or close to the so-called rifampin resistance clusters of rpoB(R) plays a key role in fundamental activities of the RNA polymerase. The rpoB(R)-specific missense mutation H426N is essential for the activation of secondary metabolism, molecular mechanism, overview
-
-
-
additional information
?
-
-
bacterial anti-sigma factors typically regulate sigma factor function by restricting the access of their cognate sigma-factors to the RNA polymerase RNAP core enzyme, regulation of RNAP holoenzyme, Esigma70, involving Rsd and the Rsd orthologue AlgQ, a global regulator of gene expression in Pseudomonas aeruginosa, which simultaneously interact with conserved region 2 and region 4 of sigma70 mediated by separate surfaces of Rsd, interaction with mutants of Rsd and AlgQ, mechanism, detailed overview. Rsd can strongly regulate the production of the Pseudomonas aeruginosa virulence factor pyocyanin in a manner that depends on their abilities to interact with sigma70 region 2
-
-
-
additional information
?
-
-
molecular mechanisms enabling sigma factor PvdS, directing the transcription of pyoverdine and virulence genes under iron limitation, to compete with the major sigma RpoD for RNA polymerase binding, overview
-
-
-
additional information
?
-
-
multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions
-
-
-
additional information
?
-
P04050
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, overview
-
-
-
additional information
?
-
-
RNAP function through the transcription cycle with initiation/re-initiation, elongation, and termination, detailed overview
-
-
-
additional information
?
-
-
RNAPII recruits COMPASS, a histone methyltransferase, as well as the regulator Paf1C, to the transcription active site causing methylation of histone H3K4 in a transcription-dependent manner. The large RNAPII subunit Rpb1 attracts FACT, a transcription factor that FACT participates in regulation of DNA repair and replication, to the transcription site, and Rpb1 also interacts with RSC, an abundant Swi/Snf-like chromatin remodeling complex with multiple subunits, and other general transcription factors, as well as with histone chaperone proteins, mRNA processing and export factors, DNA repair factors, protein kinases, and other cellular proteins, overview
-
-
-
additional information
?
-
-
the phosphatase activity of Cdc14 is required for Pol I inhibition, transcription inhibition is necessary for complete chromosome disjunction, because rRNA transcripts block condensin binding to rDNA, and show that bypassing the role of Cdc14 in nucleolar segregation requires in vivo degradation of nascent transcripts, transcription interferes with chromosome condensation, not the reverse
-
-
-
additional information
?
-
-
the Switch 1 loop of RNA polymerase II, located at the downstream end of the transcription bubble, may operate as a specific sensor of the nucleoside triphosphates available for transcription. Regulatory effects of RNA polymerase II on URA2 gene, encoding the rate-limiting enzyme of UTP biosynthesis after activation by UTP shortage, RNA polymerase II occupancy is increased on the URA2 open reading frame, overview
-
-
-
additional information
?
-
-
mitochondrial RNA polymerase (Rpo41) and its transcription factor (Mtf1) are an efficient primase that initiates DNA synthesis on ssDNA coated with the yeast mitochondrial ssDNA-binding protein, Rim1. Both Rpo41 and Rpo41-Mtf1 can synthesize short and long RNAs on ssDNA template and prime DNA synthesis by the yeast mitochondrial DNA polymerase Mip1. Regarding the RNA-DNA products, Rpo41 and Rpo41-Mtf1 have slightly different priming specificity. Both prefer to initiate with ATP from short priming sequences such as 3'-TCC, TTC, and TTT, and the consensus sequence is 3'-Pu(Py)2-3
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additional information
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multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions
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additional information
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RNAP function through the transcription cycle with initiation/re-initiation, elongation, and termination, detailed overview
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additional information
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multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions
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additional information
?
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RNAP function through the transcription cycle with initiation/re-initiation, elongation, and termination, detailed overview
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additional information
?
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multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions
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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
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
-
can replace Mg2+ in activation, 10% of the activity observed with Mg2+
Iron
K+
KCl
Mg2+
Mn2+
Zinc
-
a conserved zinc binding domain in the largest subunit of DNA-dependent RNA polymerase modulates intrinsic transcription termination and antitermination but does not stabilize the elongation complex
additional information
Iron
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RNA polymerase is a member of the iron-sulfur cluster protein family and contains two 4Fe-4S cluster binding motifs
Iron
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RNA polymerase is a member of the iron-sulfur cluster protein family
Iron
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RNA polymerase is a member of the iron-sulfur cluster protein family
Iron
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RNA polymerase is a member of the iron-sulfur cluster protein family and contains one 4Fe-4S cluster binding motif
Iron
Q980R2 and P58192 and Q980R1 and P95989 and Q980A3 and Q9UXD9 and Q980L5 and Q980Q9 and Q97ZJ9 and Q980K0 and Q980Z8 and Q97ZX7 and Q980B8
the enzyme possesses a unique Fe-S cluster
Iron
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RNA polymerase is a member of the iron-sulfur cluster protein family and contains one 4Fe-4S cluster binding motif
KCl
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optimal activity at pH 8.5 is obtained in presence of 18 mM MgCl2, 200 mM KCl, 1 mM thermine and 1 mM spermidine
Mg2+
-
highest activity is obtained with 20 mM Mg2+ on poly(dA-dT) DNA or Clostridium acetobutylicum DNA as template, with calf thymus DNA as template maximal activity is achieved with 10 mM Mg2+
Mg2+
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the active center of the enzyme involves a symmetrical pair of Mg2+ ions that switch roles in synthesis and degradation. One ion is retained permanently and the other is recruited ad hoc for each act of catalysis. The weakly bound Mg2+ is stabilized in the active center in different modes depending on the type of reaction: during synthesis by the beta,gamma-phosphates of the incoming substrate and during hydrolysis by the phosphates of a non-base-paired nucleoside triphosphate
Mg2+
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two ions are required for polymerase-catalyzed nucleotide incorporation, binding structure, overview
Mg2+
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30 mM Mg2+ or 5 mM Mn2+ work equally well for maximal activity
Mg2+
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the enzyme active site is located on the back wall of the channel, where an essential Mg2+ ion is chelated by three Asp of the absolutely conserved NADFDGD motif in the A' subunit
Mg2+
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optimal activity at pH 8.5 is obtained in presence of 18 mM MgCl2, 200 mM KCl, 1 mM thermine and 1 mM spermidine
Mg2+
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higher error ratios in transcription by RNA polymerase II are observed in the presence of Mn2+ compared to Mg2+
Mn2+
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3 mM Mn2+ results in comparable activity with poly(dA-dT) DNA but reduced activity on calf thymus DNA or Clostridium acetobutylicum DNA and Clostridium acetobutylicum DNA as substrated, compared to Mg2+ activition
Mn2+
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30 mM Mg2+ or 5 mM Mn2+ work equally well for maximal activity
Mn2+
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higher error ratios in transcription by RNA polymerase II are observed in the presence of Mn2+ compared to Mg2+
additional information
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KCl, ZnCl2 and CaCl2 can not replace MgCl2 in the assay mixture
additional information
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the Pyrococcus RNA polymerase does not contain iron-sulfur cluster binding motifs
additional information
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the Thermococcus RNA polymerase does not contain iron-sulfur cluster binding motifs
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(S)-2-((1-amino-1-oxo-3-phenylpropan-2-ylamino)methyl)-3-(4-amino phenoxy)-5-methoxy phenyl acetate
(S)-2-((1-amino-1-oxo-3-phenylpropan-2-ylamino)methyl)-5-methoxy-3-(4-nitrophenoxy)phenyl acetate
(S)-2-((1-amino-3-(4-hydroxyphenyl)-1-oxopropan-2-ylamino)methyl)-3-(4-aminophenoxy)-5-methoxyphenyl acetate
(S)-2-((1-amino-3-(4-hydroxyphenyl)-1-oxopropan-2-ylamino)methyl)-5-methoxy-3-(4-nitrophenoxy)phenyl acetate
1-(3-C-ethynyl-beta-D-ribo-pentofuranosyl)cytosine
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i.e. ECyd, TAS-106, a antitumor ribonucleoside that inhibits RNA polymerase, acts synergistically in inhibiting A-549 cancer cell growth and in tumor growth in vivo. The compound also inhibits the checkpoint-associated protein, the expression of Chk1 protein and the phosphorylation of Chk1 and Chk2, antitumour effects in combination with cisplatin, overview
1-[2-[3-(4-Chloro-3-trifluoromethylphenyl)ureido]-4-trifluoromethyl phenoxy]-4,5-dichlorobenzene sulfonic acid
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2-([[(1S)-2-amino-1-(4-hydroxybenzyl)-2-oxoethyl]amino]methyl)-5-methoxy-3-(4-nitrophenoxy)phenyl acetate
3'-ethynylcytidine-5'-triphosphate
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i.e. ECTP, competitive inhibition in the presence of isolated nuclei from FM3A mouse tumor cells
4-[2-([[(1S)-2-amino-1-(4-hydroxybenzyl)ethyl]amino]methyl)-5-methoxy-3-(2-oxopropyl)benzyl]benzaldehyde
B2 RNA
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the about 180-nt B2 RNA potently represses mRNA transcription by binding tightly to RNA polymerase II and assembling with it into complexes on promoter DNA, where it keeps the polymerase from properly engaging the promoter DNA. The C-terminal domain of the largest Pol II subunit is not involved. B2 RNA binds Pol II and assembles into complexes at promoters. Binding site anaylsis usig Pol II peptides, binding structure, and mechanism of transcriptional repression by B2 RNA, detailed overview
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breast cancer susceptibility gene 1
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BRCA1, inhibits RNA pol III via inhibition of the essential transcription factor TFIIIB, mechanism, overview. BRCA1 is a tumor suppressor playing a role in DNA repair, cell cycle regulation, apoptosis, genome integrity, and ubiquitination, and it BRCA1 has a conserved N-terminal RING domain, an activation domain 1, AD1, and an acidic C-terminal domain, BRCA1 C-terminal region. Interaction with TFIIIB occurs via the BRCA1 C-terminal region domain of Fcp1p, an RNA polymerase II phosphatase. RNA pol III inhibition involves the TFIIB family members Brf1 and Brf2, overview
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CBR703
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the IC50s values are significantly decreased with template Kool NC-45, or increased with template poly(dA-dT)
Cdc14
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a protein phosphatase required for nucleolar segregation and mitotic exit4, inhibits RNA polymerase I, the phosphatase activity of Cdc14 is required for Pol I inhibition in vitro and in vivo involving nucleolar exclusion of Pol I subunits
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d(Ap4C)
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d(Ap4T), d(Ap4C) and d(Ap4G) inhibit the incorporation of dATP into DNA less effectively than d(Ap4T), d(Tp4T) and d(Tp4C) the dTTP incorporation
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d(Ap4G)
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d(Ap4T), d(Ap4C) and d(Ap4G) inhibit the incorporation of dATP into DNA less effectively than d(Ap4T), d(Tp4T) and d(Tp4C) the dTTP incorporation
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d(Ap4T)
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d(Ap4T), d(Ap4C) and d(Ap4G) inhibit the incorporation of dATP into DNA less effectively than d(Ap4T), d(Tp4T) and d(Tp4C) the dTTP incorporation
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d(Tp4C)
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d(Ap4T), d(Ap4C) and d(Ap4G) inhibit the incorporation of dATP into DNA less effectively than d(Ap4T), d(Tp4T) and d(Tp4C) the dTTP incorporation
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d(Tp4T)
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d(Ap4T), d(Ap4C) and d(Ap4G) inhibit the incorporation of dATP into DNA less effectively than d(Ap4T), d(Tp4T) and d(Tp4C) the dTTP incorporation
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etoposide
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treatment with 0.02 mM etoposide leads to a transient inhibition of rRNA synthesis
ML-60218
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treatment of A-549 cells with the Pol III inhibitor ML-60218 decreased the cytosolic RNA:DNA hybrid staining
oxygen
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the enzyme is highly oxygen sensitive. Inactivation is accompanied by cross-linking of components. Inactivated enzyme can be reactivated by reduction with sodium dithionite
per-O-acetyl-verbascoside
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compound isolated from aerial part of Buddleja cordobensis Grisebach, most active among the compounds tested
procyclin-associated genes
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i.e. PAG1, PAG2 or PAG3, inhibit RNA synthesis, deletion of PAGs lead to increased mRNA levels, regulation of PAG expressions, overview
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protein Rim1
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the ssDNA-binding protein Rim1 severely inhibits theRNAsynthesis activity of Rpo41, but not the Rpo41-Mtf1 complex, which continues to prime DNA synthesis efficiently in the presence of Rim1
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protein TLS
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translocated in liposarcoma, a protein originally identified as the product of a chromosomal translocation, which associates with both RNAP II and the spliceosome, also represses transcription by RNAP III. It represses transcription from all three classes of RNAP III promoters in vitro and to associates with RNAP III genes in vivo. Depletion of TLS by siRNA in HeLa cells resulted in increased steady-state levels of RNAP III transcripts as well as increased RNAP III and TBP occupancy at RNAP III-transcribed genes
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RECQL5
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a DNA helicase of the RECQ family, directly inhibits RNA polymerase II. It RECQL5 inhibits both initiation and elongation in transcription assays reconstituted with highly purified general transcription factors and RNAPII, RECQL5 helicase activity is not required for inhibition
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Spt5
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the large subunit of the DRB sensitivity-inducing factor, DSIF, represses or activates RNAPII elongation in vitro. CTR1 and CTR2CT, the two repeat-containing regions constituting the C-terminus of Spt5, play a redundant role in repressing RNAPII elongation in vivo, overview. Mutant NSpt5, lacking the C-terminus, directly associates with hsp70-4 chromatin in vivo and increases the occupancy of RNAPII, positive transcription elongation factor b, histone H3 Lys 4 trimethylation, and surprisingly, the negative elongation factor A at the locus, indicating a direct action of NSpt5 on the elongation repressed locus, nuclear extracts containing the constitutively active P-TEFb and WT DSIF lead to a time-dependent increase of the long, promoter-distal RNase T1-resistant products, reflecting the elongation stimulatory activity of Spt5, overview
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terminatin factor NsiI
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N-terminally FLAG-tagged fusion protein Nsi1 expressed from Sf21 insect cells. Binding of the termination factor Nsi1 to its cognate DNA site is sufficient to terminate RNA polymerase I transcription in vitro and to induce termination in vivo. Nsi1 contains Myb-like DNA binding domains and associates in vivo near the 3' end of rRNA genes to rDNA. Binding of Nsi1 to a stretch of 11 nucleotides in the correct orientation is sufficient to pause elongating Pol I shortly upstream of the Nsi1 binding site and to release the transcripts in vitro, and the same minimal DNA element triggers Nsi1-dependent termination of pre-rRNA synthesis in vivo. Termination efficiency in the in vivo system can be enhanced by inclusion of specific DNA sequences downstream of the Nsi1 binding site
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(S)-2-((1-amino-1-oxo-3-phenylpropan-2-ylamino)methyl)-3-(4-amino phenoxy)-5-methoxy phenyl acetate
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(S)-2-((1-amino-1-oxo-3-phenylpropan-2-ylamino)methyl)-3-(4-amino phenoxy)-5-methoxy phenyl acetate
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(S)-2-((1-amino-1-oxo-3-phenylpropan-2-ylamino)methyl)-5-methoxy-3-(4-nitrophenoxy)phenyl acetate
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(S)-2-((1-amino-1-oxo-3-phenylpropan-2-ylamino)methyl)-5-methoxy-3-(4-nitrophenoxy)phenyl acetate
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(S)-2-((1-amino-3-(4-hydroxyphenyl)-1-oxopropan-2-ylamino)methyl)-3-(4-aminophenoxy)-5-methoxyphenyl acetate
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(S)-2-((1-amino-3-(4-hydroxyphenyl)-1-oxopropan-2-ylamino)methyl)-3-(4-aminophenoxy)-5-methoxyphenyl acetate
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(S)-2-((1-amino-3-(4-hydroxyphenyl)-1-oxopropan-2-ylamino)methyl)-5-methoxy-3-(4-nitrophenoxy)phenyl acetate
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(S)-2-((1-amino-3-(4-hydroxyphenyl)-1-oxopropan-2-ylamino)methyl)-5-methoxy-3-(4-nitrophenoxy)phenyl acetate
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2-([[(1S)-2-amino-1-(4-hydroxybenzyl)-2-oxoethyl]amino]methyl)-5-methoxy-3-(4-nitrophenoxy)phenyl acetate
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2-([[(1S)-2-amino-1-(4-hydroxybenzyl)-2-oxoethyl]amino]methyl)-5-methoxy-3-(4-nitrophenoxy)phenyl acetate
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4-[2-([[(1S)-2-amino-1-(4-hydroxybenzyl)ethyl]amino]methyl)-5-methoxy-3-(2-oxopropyl)benzyl]benzaldehyde
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4-[2-([[(1S)-2-amino-1-(4-hydroxybenzyl)ethyl]amino]methyl)-5-methoxy-3-(2-oxopropyl)benzyl]benzaldehyde
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alpha-Amanitin
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alpha-amanitin inhibits Pol II by trapping the wedged trigger loop and shifted bridge helix, thereby stabilizing a conformation of the elongation complex that apparently represents a translocation intermediate
alpha-Amanitin
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the potent Sc RNAP II inhibitor binds to a ternary elongation complex with an open wedged conformation of the trigger loop
cisplatin
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a single cisplatin 1,2-d(CG) intrastrand cross-link or a single cisplatin 1,3-d(GTG) intrastrand cross-link is a strong block to the enzyme. The efficiency of the block at a cisplatin 1,2-d(GG) intrastrand cross-link is similar in several different nucleotide sequence contexts. Some blockage is also observed when the single cisplatin 1,3-d(GTG) intrastrand cross-link is located in the non-transcribed strand. Cisplatin-induced lesions in the transcribed DNA strand constitute a strong physical barrier to RNA polymerase progression
cisplatin
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a single cisplatin 1,2-d(CG) intrastrand cross-link or a single cisplatin 1,3-d(GTG) intrastrand cross-link is a strong block to the enzyme. The efficiency of the block at a cisplatin 1,2-d(GG) intrastrand cross-link is similar in several different nucleotide sequence contexts. Some blockage is also observed when the single cisplatin 1,3-d(GTG) intrastrand cross-link is located in the non-transcribed strand. Cisplatin-induced lesions in the transcribed DNA strand constitute a strong physical barrier to RNA polymerase progression
etnangien
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from the myxobacterium Sorangium cellulosum, a poly-unsaturated 22-membered polyketide macrolide, inhibits bacterial RNA polymerase, shows no cross-resistance to rifampicin
etnangien
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from the myxobacterium Sorangium cellulosum, a poly-unsaturated 22-membered polyketide macrolide, inhibits bacterial RNA polymerase, shows no cross-resistance to rifampicin, poor inhibition
etnangien
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from the myxobacterium Sorangium cellulosum, a poly-unsaturated 22-membered polyketide macrolide, inhibits bacterial RNA polymerase, shows no cross-resistance to rifampicin
etnangien
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from the myxobacterium Sorangium cellulosum, a poly-unsaturated 22-membered polyketide macrolide, inhibits bacterial RNA polymerase, shows no cross-resistance to rifampicin
etnangien
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from the myxobacterium Sorangium cellulosum, a poly-unsaturated 22-membered polyketide macrolide, inhibits bacterial RNA polymerase, shows no cross-resistance to rifampicin
etnangien
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from the myxobacterium Sorangium cellulosum, a poly-unsaturated 22-membered polyketide macrolide, inhibits bacterial RNA polymerase, poor inhibition of the yeast enzyme
etnangien
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from the myxobacterium Sorangium cellulosum, a poly-unsaturated 22-membered polyketide macrolide, inhibits bacterial RNA polymerase, shows no cross-resistance to rifampicin
myxopyronin
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an alpha-pyrone antibiotic, targets the RNAP switch region, which is the hinge that mediates opening and closing of the RNAP active-center cleft. Lower values for inhibition by myxopyronin in the presence of template Kool NC-45
myxopyronin
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produced by the bacteria Myxococcus fulvus, inhibits initiation of RNA polymerase transcription and binding complex structure. The compounds inhibits the enzyme also from rifamycin- or multidrug-resistant bacteria. the inhibition mechanism proceeds via inhibiting DNA binding rather than affecting transcription complex stability or processivity following DNA binding, overview
myxopyronin
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inhibits bacterial RNA polymerase and inhibits transcription on the artificially melted promoters, inhibition mechanism, overview. The antibiotic binds to a pocket deep inside the RNAP clamp head domain, which interacts with the DNA template in the transcription bubble, binding of dMyx stabilizes refolding of the beta'-subunit switch-2 segment, resulting in a configuration that might indirectly compromise binding to, or directly clash with, the melted template DNA strand, binding structure, overview. Antibiotic binding does not prevent nucleation of the promoter DNA melting but instead blocks its propagation towards the active site. dMyx binds in the pocket deep inside the RNAP clamp head domain. Mutations designed in switch-2 mimic the dMyx effects on promoter complexes in the absence of antibiotic
Streptolydigin
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the antibiotic binds to a Tt RNAP TEC with an open trigger loop
additional information
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synthesis of simplified etnangien analogues and analysis of their antimicrobial activities, overview
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additional information
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no inhibition by 0.1 mg/ml of rifampicin, streptolydigin or alpha-amanitin
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additional information
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no inhibition by ent-16-ketobeyeran-19-oic acid, i.e. isosteviol, and related compounds
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additional information
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despite relatively high overall sequence and structural homology between bacterial and mammalian core RNAP enzymes, there are sufficient differences between the enzyme classes for exploitation in the discovery of selective bacterial inhibitors
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additional information
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synthesis of simplified etnangien analogues and analysis of their antimicrobial activities, overview
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additional information
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the use of dsDNA templates containing classical promoters has only a negligible effects on the potency of enzyme inhibitors
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additional information
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FLiZ antagonize sigmaS-dependent gene expression in Escherichia coli. FliZ is an abundant DNA-binding protein and a global regulatory protein under the control of the flagellar master regulator FlhDC. It inhibits gene expression mediated by sigmaS by recognizing operator sequences that resemble the -10 region of sigmaS-dependent promoter. FLiZ plays a pivotal role in the decision between alternative life-styles, i.e. FlhDC-controlled flagellum-based motility or pS-dependent curli fimbriae-mediated adhesion and biofilm formation. FliZ is a global repressor with a DNA sequence specificity overlapping that of sigmaScontaining RNA polymerase, mechanism, overview
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additional information
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synthesis of simplified etnangien analogues and analysis of their antimicrobial activities, overview
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additional information
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inactivation of RNase P, by knockdown of RNase P subunits Rpp21, Rpp29 or Rpp38 by RNA interference, reduces the level of nascent transcription by Pol I, and more considerably that of Pol III, e.g. causing marked reduction in transcription of rDNA by Pol I
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additional information
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oncogenes and tumor suppressors control Pol I transcription, overview. Development of drugs that target the Pol I transcription machinery at different points, overveiw
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additional information
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Top1 inhibition favors Pol II escape from a promoter-proximal pausing site of the human HIF-1alpha gene in living cells. Top1 inhibition can trigger a transcriptional stress, involving antisense transcription and increased chromatin accessibility, which is dependent on cdk activity and deregulated Pol II pausing
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additional information
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POLRMT is an off target for antiviral ribonucleoside analogues, unique mechanisms of mitochondrial transcription inhibition, overview
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additional information
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synthesis of simplified etnangien analogues and analysis of their antimicrobial activities, overview
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additional information
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gamma irradiation leads to a transient inhibition of rRNA synthesis, but Pol I transcription is not blocked by DNA damage itself, but by the action of DNA repair enzymes
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additional information
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oncogenes and tumor suppressors control Pol I transcription, overview. Development of drugs that target the Pol I transcription machinery at different points, overveiw
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additional information