2.7.7.6: DNA-directed RNA polymerase
This is an abbreviated version!
For detailed information about DNA-directed RNA polymerase, go to the full flat file.
Word Map on EC 2.7.7.6
-
2.7.7.6
-
chromatin
-
histone
-
rrna
-
strand
-
rnaps
-
nucleosome
-
tata
-
drosophila
-
pausing
-
pre-mrnas
-
tbp
-
nucleolar
-
bacteriophage
-
polyadenylation
-
single-stranded
-
cyclin-dependent
-
holoenzyme
-
cyclin
-
spacers
-
helicase
-
fidelity
-
polya
-
coactivator
-
protein-coding
-
transactivation
-
adenovirus
-
xenopus
-
ribonucleoproteins
-
sequence-specific
-
stall
-
pause
-
chip-seq
-
vaccinia
-
multisubunit
-
ribozyme
-
heptapeptide
-
duplex
-
h3k4me3
-
spliceosome
-
nucleoplasm
-
run-on
-
supercoiled
-
trimethylation
-
subcomplexes
-
exonuclease
-
heterochromatin
-
translesion
-
medicine
-
primase
-
molecular biology
-
analysis
-
diagnostics
-
drug development
-
misincorporation
-
proofread
-
synthesis
- 2.7.7.6
- chromatin
- histone
- rrna
- strand
-
rnaps
- nucleosome
- tata
- drosophila
-
pausing
- pre-mrnas
- tbp
-
nucleolar
- bacteriophage
-
polyadenylation
-
single-stranded
-
cyclin-dependent
-
holoenzyme
- cyclin
-
spacers
- helicase
-
fidelity
- polya
-
coactivator
-
protein-coding
-
transactivation
- adenovirus
- xenopus
- ribonucleoproteins
-
sequence-specific
-
stall
-
pause
-
chip-seq
- vaccinia
-
multisubunit
-
ribozyme
- heptapeptide
- duplex
-
h3k4me3
-
spliceosome
- nucleoplasm
-
run-on
-
supercoiled
-
trimethylation
-
subcomplexes
-
exonuclease
- heterochromatin
-
translesion
- medicine
- primase
- molecular biology
- analysis
- diagnostics
- drug development
-
misincorporation
-
proofread
- synthesis
Reaction
Synonyms
C RNA formation factors, chloroplast soluble RNA polymerase, deoxyribonucleic acid-dependent ribonucleic acid polymerase, DNA-dependent ribonucleate nucleotidyltransferase, DNA-dependent RNA nucleotidyltransferase, DNA-dependent RNA polymerase, DNA-dependent RNA polymerase I, DNA-dependent RNA polymerase III, DNA-dependent RNAP, h-mtRNAP, K1E RNAP, mitochondrial RNA polymerase, mitoRNAP, More, mtRNAP, multi-subunit RNA polymerase, nucleotidyltransferase, ribonucleate, plastid RNA polymerase, plastid-encoded polymerase, plastid-encoded RNA polymerase, Pol I, Pol II, pol III, Pol IIIalpha, Pol IIIbeta, Pol IV, Pol V, polI, PolIII, POLRMT, ribonucleate nucleotidyltransferase, ribonucleate polymerase, ribonucleic acid formation factors, C, ribonucleic acid nucleotidyltransferase, ribonucleic acid polymerase, ribonucleic acid transcriptase, ribonucleic polymerase, ribonucleic transcriptase, rifampicin-resistant RNA polymerase, RNA formation factors, C, RNA nucleotidyltransferase, RNA nucleotidyltransferase (DNA-directed), RNA pol III, RNA polymerase, RNA polymerase core enzyme, RNA polymerase I, RNA polymerase II, RNA polymerase II complex, RNA polymerase III, RNA polymerase III complex, RNA transcriptase, RNAP, RNAP core enzyme, RNAP I, RNAP II, RNAP III, RNAP sigma70, RNAP-II, RNAP2, RNAPII, RPO, rpo1N, Rpo41, RpoA, RpoD, RpoS, RpoT, Saci_0834, sigma38 RNA polymerase, sigmaS-containing RNA polymerase, T7 RNA polymerase, T7 RNAP, T7-like RNA polymerase, Taq polymerase, transcriptase, YonO
ECTree
2.7.7.6 DNA-directed RNA polymeraseAdvanced search results
results (
results (Substrates Products
Substrates Products on EC 2.7.7.6 - DNA-directed RNA polymerase
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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
-
-
?
DNA + 5-[[[2-(1H-indol-3-yl)ethyl]amino]carbonyl]-1-deazaUTP
?
-
-
-
-
?
nucleoside triphosphate + A10G2A2C2C
?
-
oligonucleotide extension
-
-
?
nucleoside triphosphate + T10G2T2C2C
?
-
oligonucleotide extension
-
-
?
ATP + RNAn
diphosphate + RNAn+1
the primer can be extended only in the presence of ATP. The length of the double-stranded region of RNA/DNA duplexes is important for the primer extension. The length of the double-stranded region of RNA/DNA duplexes is important for the primer extension performed by the enzyme. Under these in vitro conditions POLRMT has a preference for P/T duplexes with short hybridization regions
-
-
?
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
-
-
-
-
?
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
-
DNA templates containing smaller base modifications in 2'-deoxyribonucleoside triphosphates (H, Me in 7-deazapurines) are perfectly tolerated whereas bulky modifications (Ph at any nucleobase) and uracil blocked transcription. Some middle-sized modifications (vinyl or ethynyl) are partly tolerated. In all cases where the transcription proceeds, full length RNA product with correct sequence is obtained indicating that the modifications of the template are not mutagenic and the inhibition is probably at the stage of initiation
-
-
?
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
-
various DNA lesions significantly affect the efficiency and fidelity of RNA synthesis. DNA modifications that disrupt correct base-pairing can strongly inhibit transcription and increase nucleotide misincorporation by RNAP. The universal transcription factor GreA and Deinococcus-specific factor Gfh1 stimulate RNAP stalling at various DNA lesions, depending on the type of the lesion and the presence of Mn2+ ions
-
-
?
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 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
the alpha subunit C-terminal domain of Escherichia coli RNA polymerase (alphaCTD) recognizes the upstream promoter(UP) DNA element via its characteristic minor groove shape and electrostatic potential
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
the alpha subunit C-terminal domain of Escherichia coli RNA polymerase (alphaCTD) recognizes the upstream promoter(UP) DNA element via its characteristic minor groove shape and electrostatic potential
-
-
?
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
-
-
-
-
?
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
Inovirus M13
-
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 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
Mycolicibacterium 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
Q980R2; P58192; Q980R1; P95989; Q980A3; Q9UXD9; Q980L5; Q980Q9; Q97ZJ9; Q980K0; Q980Z8; Q97ZX7; Q980B8
-
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
Q980R2; P58192; Q980R1; P95989; Q980A3; Q9UXD9; Q980L5; Q980Q9; Q97ZJ9; Q980K0; Q980Z8; Q97ZX7; Q980B8
-
-
-
?
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
-
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
-
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
?
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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
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additional information
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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
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additional information
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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
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additional information
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molecular mechanisms of transcription regulation in mitochondria, molecular organization of the human mitochondrial transcription initiation complex, overview
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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
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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
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TLS regulates both RNAPs II and III and supports the possibility that cross-regulation between RNA polymerases is important in maintaining normal cell growth
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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
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negative DNA supercoiling favors the induction of unpaired regions at some sequence motifs on dsDNA, substrate specificity and structural effects on activity, overview
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RNA polymerase III transcribes small untranslated RNAs that include tRNAs, 5S RNA, U6 RNA, and some microRNAs
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the B2 family of short interspersed elements is transcribed into non-coding RNA by RNA polymerase III
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POLRMT can act as a primase in vitro and support lagging-strand DNA synthesis on a small 70 bp minicircle, overview
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incorporation of 2'-dATP or 2'-F-ATP does not lead to immediate chain termination, but the enzyme can not add the second 2'-dATP or 2'-F-ATP to the synthesized RNA
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additional information
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incorporation of 2'-dATP or 2'-F-ATP does not lead to immediate chain termination, but the enzyme can not add the second 2'-dATP or 2'-F-ATP to the synthesized RNA
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Inovirus M13
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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
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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
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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
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active site structure formed by amino acids from two domains: Palm with Asp457 and Asp695, and Fingers with Tyr537 and Lys529, overview
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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
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additional information
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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
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additional information
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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
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Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
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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
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additional information
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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
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additional information
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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
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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
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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
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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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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
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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
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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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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
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RNAP function through the transcription cycle with initiation/re-initiation, elongation, and termination, detailed overview
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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
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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
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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
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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
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additional information
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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
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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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quantitative reverse transcriptase-PCR expression analysis
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quantitative reverse transcriptase-PCR expression analysis
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determination of the substrate binding site
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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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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
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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 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
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additional information
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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
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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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in vitro transcriptional activity of recombinant assembled Xcc RNAP, overview
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in vitro transcriptional activity of recombinant assembled Xcc RNAP, overview
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additional information
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in vitro transcriptional activity of recombinant assembled Xcc RNAP, overview
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additional information
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in vitro transcriptional activity of recombinant assembled Xcc RNAP, overview
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