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Information on EC 2.7.7.6 - DNA-directed RNA polymerase and Organism(s) Saccharomyces cerevisiae and UniProt Accession P04050
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2.7.7.6 DNA-directed RNA polymeraseIUBMB Comments
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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Word Map
- 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
The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
rna polymerase ii, pol ii, t7 rna polymerase, rna polymerase i, pol iii, rna polymerase iii, pol i, rnapii, rnap ii, dna-dependent rna polymerase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
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
nucleotidyltransferase, ribonucleate
-
-
-
-
Pol II
ribonucleate nucleotidyltransferase
-
-
-
-
ribonucleate polymerase
-
-
-
-
ribonucleic acid formation factors, C
-
-
-
-
ribonucleic acid nucleotidyltransferase
-
-
-
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ribonucleic acid polymerase
-
-
-
-
ribonucleic acid transcriptase
-
-
-
-
ribonucleic polymerase
-
-
-
-
ribonucleic transcriptase
-
-
-
-
RNA formation factors, C
-
-
-
-
RNA nucleotidyltransferase
-
-
-
-
RNA nucleotidyltransferase (DNA-directed)
-
-
-
-
RNA polymerase
RNA polymerase I
RNA polymerase II
RNA polymerase III
RNA transcriptase
-
-
-
-
RNAP
RNAP I
-
-
-
-
RNAP II
RNAP III
-
-
-
-
transcriptase
-
-
-
-
additional information
-
RNA polymerase is a member of the iron-sulfur cluster protein family
DNA-dependent RNA polymerase
-
-
-
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Pol II
-
-
-
-
RNA polymerase
-
-
-
-
RNA polymerase I
-
-
-
-
RNA polymerase II
-
-
-
-
RNA polymerase II
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RNA polymerase III
-
-
-
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RNAP
-
-
-
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RNAP II
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-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
nucleotidyl group transfer
-
-
-
-
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).
CAS REGISTRY NUMBER
COMMENTARY
9014-24-8
-
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
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
-
?
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
?
-
-
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
?
-
-
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
-
-
?
NATURAL SUBSTRATE
NATURAL 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
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
-
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA
-
-
?
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
?
-
-
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
?
-
-
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
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Iron
-
RNA polymerase is a member of the iron-sulfur cluster protein family
Mg2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Cdc14
-
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
-
etnangien
-
from the myxobacterium Sorangium cellulosum, a poly-unsaturated 22-membered polyketide macrolide, inhibits bacterial RNA polymerase, poor inhibition of the yeast enzyme
protein Rim1
-
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
-
terminatin factor NsiI
-
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
-
alpha-Amanitin
-
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
-
the potent Sc RNAP II inhibitor binds to a ternary elongation complex with an open wedged conformation of the trigger loop
additional information
-
a relatively short DNA region, lost in up2DELTA mutant and located immediately upstream of the URA2 initiator, impairs URA2 transcription by preventing RNA polymerase II from progressing towards the URA2open reading frame
-
additional information
-
synthesis of simplified etnangien analogues and analysis of their antimicrobial activities, overview
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ctk1
-
the kinase is required for the stability of the scaffold, but Ctk1 kinase activity is not required for the dissociation of basal transcription factors
-
TFIIIE
-
a basal transcription factor, complexes with several ribosomal proteins and enhances tRNA and 5S rRNA transcription of the RNA polymerase, regualtion, overview
-
TFIIS
-
an RNA cleavage stimulatory factor TFIIS. 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
-
Pol III initiates and reinitiates transcription in the absence or presence of transcription factors, during the first transcription cycle transcription factors IIIB and IIIC mainly contribute to the selectivity and not to the rate of Pol III association to the template, while their stable association with the promoter in subsequent cycles strongly contributes to the high rate of transcription reinitiation by Pol III
-
additional information
-
the enzyme complex requires basal transcription factors, i.e. TFIID, TFIIA, TFIIH, and TFIIE, for complete processing of transitions from initiation to elongation, overview
-
additional information
-
the Pol II transcription apparatus requires the transcription factors TBP, TFIIB, TFIIEalpha and TFIIS
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
distribution of TFIIB, TFIIH and RNA polymerase II at the URA2 locus, RNA polymerase II occupancy is increased on the URA2 open reading frame, overview
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
evolution
-
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
malfunction
physiological function
additional information
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
-
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
physiological function
-
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
-
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 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
-
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
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
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
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dodecamer
oligomer
-
RNAPII structure and modeling of the multi-subunit enzyme complex, RNAP subunits can be divided into three groups concerned with catalysis, assembly of the catalytic subunits and auxiliary functions, overview
additional information
dodecamer
-
the Rpb2 subunit of RNAP II combines with the Rpb1 subunit to form the RNAP II active site. RNAP II is isolated as a 12 subunit enzyme, Rpb1-Rpb12
additional information
peptide regions that interact with regulatory factors are close to the Pol II surface and assume seemingly flexible loop structures, one is located in the TFIIF-interacting protrusion domain, the other is located in the TFIIE-interacting clamp domain, conformations, e.g. of the TFIIF-interacting Rpb2 protrusion, overview. Conformational movement and dynamics of fork loop-1 and -2. mechanism, overview
additional information
-
analysis of interaction sbetween the largest subunit Rpb1 and the other subunits, overview
additional information
-
conformational plasticity of the active center and importance of the bridge helix structure for enzyme activity, overview
additional information
-
detailed RNAPII structure study in different comformations, e.g. concerning the trigger loop, using crystal structures, the collective set of all normal modes describes enzyme flexibility as a function of residue in terms of root mean square fluctuations, RMSF values are directly related to crystallographic B-factors, enzyme motions described by individual modes, caclulations, overview
additional information
-
secondary structure and organization of multi-subunit DNA-dependent RNA polymerases, overview. The Rpb8/G RNA polymerase subunit is restricted to eukaryotes and Crenarchaea
additional information
-
the enzyme consists of three distinct regions, a catalytic C-terminal polymerase domain, an N-terminal domain and an N-terminal extension, a pentatricopeptide repeat domain is not present in the yeast enzyme
additional information
-
the C-terminal domain (CTD) of RNA polymerase II in eukaryotes is comprised of tandemly repeating units of a conserved seven-amino acid sequence. DNA instability may play a role in regulating or maintaining C-terminal domain repeat number. 36 diverse Saccharomyces cerevisiae isolates reveal evidence of numerous past rearrangements within the DNA sequence that encodes the C-terminal domain, the total number of CTD repeats is relatively static (24-26 repeats in all strains), suggesting a balancing act between repeat expansion and contraction. Presence of DNA secondary structures, specifically G-quadruplex-like DNA,within the CTD coding region. Mutating PIF1, a G-quadruplex-specific helicase, results in increased CTD repeat length polymorphisms. RAD52 is necessary for CTD repeat expansion but not contraction, identifying a role for recombination in repeat expansion
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
phosphoprotein
-
the yeast Ctk1 kinase associates with elongation complexes and phosphorylates serine 2 in the YSPTSPS repeats of the RNApII large subunit Rpb1 C-terminal domain, a modification that is necessary for efficient recruitment of the Set2 methyltransferase to RNApII within transcribed regions and for coupling transcription to mRNA 3'-end processing, but Ser2 phosphorylation of the Rpb1 CTD does not regulate the 5' transitions. Ctk1 kinase activity is not required for the dissociation of basal transcription factors
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified Pol II, X-ray diffraction structuredetermination and analysis at 3.8 A resolution, single anomalous diffraction from zinc ions bound intrinsically in Pol II
crystallization of RNA polymerase II elongation complex. The purified paused complex forms crystals capable of X-ray diffraction to 3,5 A resolution. The complex remains active in the crystal and, in the presence of nucleoside triphosphates, can efficiently extend the transcript in situ
-
crystals are grown by the sitting drop vapor diffusion method, crystal structure of RNA polymerase II in the act of transcription is determined at 3.3 A resolution
-
glycerol precipitation, two-dimensional crystals of RNA polymerase I dimers are obtained upon interaction with positively charged lipid layers
-
hanging-drop vapour diffusion method. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS
-
in complex with alpha-amanitin, hanging drop vapour diffusion method, with 200 mM ammonium acetate, 300 mM sodium acetate, 50 mM HEPES, pH 7.0, 4-7% (w/v) PEG 6000 and 5 mM Tris(2-carboxyethyl) phosphine
-
in order to obtain an atomic model of the complete Pol II, atomic models of the core Pol II at 2.8 A resolution and of the additional heterodimeric subcomplex of subunits Rpb4 and Rpb7 at 2.3 A resolution are combined and refined against the diffraction data obtained from a holo-Pol II crystal at 3.8 A resolution, method optimization
-
two-dimensional crystals are obtained by interaction with positively charged lipid layers. The enzyme is preferentially oriented by the lipid phase
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D505A
-
mutation in subunit Rpb2, the mutant shows a weak defect in the escape from a transcriptional stall at A20
E1028Q
-
mutation in subunit Rpb2, the mutant shows transcription elongation defects
E529A
E529D
E529Q
-
the substitution mutant is are slower than the wild-type enzyme in RNA elongation
G985A/G987A
-
the double substitution in subunit Rpb2 is expected to subtly affect the conformation and/or dynamics of K987, an essential residue
Q513A
-
mutation in subunit Rpb2, the mutant shows a weak defect in the escape from a transcriptional stall at A20
R512A
-
mutation in subunit Rpb2, the mutant shows transcription elongation defects
R512C
R766A
-
the substitution is lethal, consistent with an important role for this invariant latch residue
R766Q
-
the substitution is lethal, consistent with an important role for this invariant latch residue
additional information
E529A
-
mutation in subunit Rpb2, the mutant is faster in elongation compared to wild type RNAP II
E529A
-
the substitution mutant is are faster than the wild-type enzyme in RNA elongation
E529D
-
mutation in subunit Rpb2, the mutant is faster in elongation compared to wild type RNAP II
E529D
-
the substitution mutant is are faster than the wild-type enzyme in RNA elongation
R512C
-
mutation in subunit Rpb2, the mutant shows transcription elongation defects
R512C
-
site-directed mutagenesis, the highly conserved residue is located about 20 A from Mg2+-I and just C-terminal to the fork loop, molecular dynamics simulations, overview. Mutant Sc Rpb2 R512C is slow in elongation and shows transcriptional defects. Rpb2 R512C may have a defect in CTP-Mg2+ sequestration
additional information
-
mutagenesis by amino-acid replacements altering the RNA polymerase II Switch 1 loop domain, such as rpb1-L1397S. rpb1-L1397S enhances RNA polymerase II occupancy downstream of the URA2 initiator
additional information
-
mutations are made in highly conserved residues Rpb2 K979, K987, and R1020 within the active site region of RNAP II, at positions that potentially might be essential for catalytic function. Mutations are constructed in an extended fork region of subunit Rpb2, residues R504-E529, construction of diverse mutant strains, e.g. strain yBC-9 expressing subunit Rpb2 under the control of the Gal promoter and is deleted for the chromosomal copy of the DST1 gene, encoding transcription factor IIS, TFIIS. From the strain yBC-9, the strain yBC-32 was constructed by transformation with pFL39-RPB2-TAP, TRP1
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
the two largest Pol I subunits do not dissociate from one another between rounds of transcription. Pol I is relatively stable through multiple rounds of transcription
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant wild-type ProtA-tagged enzyme PolI from strain y2423 by protein A affinity chromatography and cleavage of the ProtA tag by TEV protease
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
C-terminal domain encoding DNA and amino acid sequence determination and analysis, genotyping, sequence comparisons of the CTD region from 36 yeast strains. The DNA helicase Pif1 suppresses CTD rearrangement
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recombinant expression of wild-type ProtA-tagged enzyme PolI in strain y2423. The second largest subunit of one polymerase is expressed as a C-terminal fusion protein with a protein A tag. Between the C terminus of the subunit and the protein A part, a recognition site for TEV protease is located
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recombinant Rpb2 R512C, TAP-tagged at the C-terminus of the RNAP II Rpb9 subunit
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RPB2 gene encoding the Rpb2 subunit of yeast RNAP II, expression of mutant enzyme and subunits in Escherichia coli strain XL-1 Blue
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
molecular biology
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Rpo41-Mtf1 is an attractive candidate for serving as the primase to initiate lagging strand DNA synthesis during normal replication and/or to restart stalled replication from downstream ssDNA
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Edwards, A.M.; Darst, S.A.; Feaver, W.J.; Thompson, N.E.; Burgess, R.R.; Kornberg, R.D.
Purification and lipid-layer crystallization of yeast RNA polymerase II
Proc. Natl. Acad. Sci. USA
87
2122-2126
1990
Saccharomyces cerevisiae
Steinberg, T.H.; Mathews, D.E.; Durbin, R.D.; Burgess, R.R.
Tagetitoxin: a new inhibitor of eukaryotic transcription by RNA polymerase III
J. Biol. Chem.
265
499-505
1990
Bombyx mori, Bos taurus, Saccharomyces cerevisiae, Homo sapiens, Xenopus laevis
Schultz, P.; Celia, H.; Riva, M.; Darst, S.A.; Colin, P.; Kornberg, R.D.; Sentenac, A.; Oudet, P.
Structural study of the yeast RNA polymerase A electron microscopy of lipid-bound molecules and two-dimensional crystals
J. Mol. Biol.
216
353-362
1992
Saccharomyces cerevisiae
Gnatt, A.L.; Cramer, P.; Fu, J.; Bushnell, D.A.; Kornberg, R.D.
Structural basis of transcription: An RNA polymerase II elongation complex at 3.3 A resolution
Science
292
1876-1881
2001
Saccharomyces cerevisiae
Schultz, P.; Celia, H.; Riva, M.; Sentenac, A.; Oudet, P.
Three-dimensional model of yeast RNA polymerase I determined by electron microscopy of two-dimensional crystals
EMBO J.
12
2601-2607
1993
Saccharomyces cerevisiae
Gnatt, A.; Fu, J.; Kornberg, R.D.
Formation and crystallization of yeast RNA polymerase II elongation complexes
J. Biol. Chem.
272
30799-30805
1997
Saccharomyces cerevisiae
Kettenberger, H.; Armache, K.J.; Cramer, P.
Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS
Mol. Cell
16
955-965
2004
Saccharomyces cerevisiae
Schneider, D.A.; Nomura, M.
RNA polymerase I remains intact without subunit exchange through multiple rounds of transcription in Saccharomyces cerevisiae
Proc. Natl. Acad. Sci. USA
101
15112-15117
2004
Saccharomyces cerevisiae
Ferrari, R.; Dieci, G.
The transcription reinitiation properties of RNA polymerase III in the absence of transcription factors
Cell. Mol. Biol. Lett.
13
112-118
2008
Saccharomyces cerevisiae
Brueckner, F.; Cramer, P.
Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation
Nat. Struct. Mol. Biol.
15
811-818
2008
Saccharomyces cerevisiae
Brueckner, F.; Armache, K.J.; Cheung, A.; Damsma, G.E.; Kettenberger, H.; Lehmann, E.; Sydow, J.; Cramer, P.
Structure-function studies of the RNA polymerase II elongation complex
Acta Crystallogr. Sect. D
65
112-120
2009
Saccharomyces cerevisiae
Dieci, G.; Ruotolo, R.; Braglia, P.; Carles, C.; Carpentieri, A.; Amoresano, A.; Ottonello, S.
Positive modulation of RNA polymerase III transcription by ribosomal proteins
Biochem. Biophys. Res. Commun.
379
489-493
2009
Saccharomyces cerevisiae
Grohmann, D.; Hirtreiter, A.; Werner, F.
Molecular mechanisms of archaeal RNA polymerase
Biochem. Soc. Trans.
37
12-17
2009
Saccharomyces cerevisiae, Saccharolobus solfataricus, Thermus aquaticus
Menche, D.; Li, P.; Irschik, H.
Design, synthesis and biological evaluation of simplified analogues of the RNA polymerase inhibitor etnangien
Bioorg. Med. Chem. Lett.
20
939-941
2009
Corynebacterium glutamicum, Saccharomyces cerevisiae, Escherichia coli, Micrococcus luteus, Staphylococcus aureus, Mycolicibacterium phlei, Gordonia rubripertincta
Sousa, R.
Tie me up, tie me down: inhibiting RNA polymerase
Cell
135
205-207
2008
Saccharomyces cerevisiae, Thermus thermophilus
Svetlov, V.; Nudler, E.
Macromolecular micromovements: how RNA polymerase translocates
Curr. Opin. Struct. Biol.
19
701-707
2009
Saccharomyces cerevisiae, Escherichia coli, Thermus thermophilus, Saccharolobus solfataricus, Thermus aquaticus
Hirata, A.; Murakami, K.S.
Archaeal RNA polymerase
Curr. Opin. Struct. Biol.
19
724-731
2009
Archaeoglobus fulgidus, Saccharomyces cerevisiae, Homo sapiens, Methanocaldococcus jannaschii, Pyrococcus furiosus, Thermococcus kodakarensis, Schizosaccharomyces pombe, Saccharolobus shibatae, Saccharolobus solfataricus
Ahn, S.H.; Keogh, M.C.; Buratowski, S.
Ctk1 promotes dissociation of basal transcription factors from elongating RNA polymerase II
EMBO J.
28
205-212
2009
Saccharomyces cerevisiae
Meyer, P.A.; Ye, P.; Suh, M.H.; Zhang, M.; Fu, J.
Structure of the 12-subunit RNA polymerase II refined with the aid of anomalous diffraction data
J. Biol. Chem.
284
12933-12939
2009
Saccharomyces cerevisiae (P04050)
Clemente-Blanco, A.; Mayan-Santos, M.; Schneider, D.A.; Machin, F.; Jarmuz, A.; Tschochner, H.; Aragon, L.
Cdc14 inhibits transcription by RNA polymerase I during anaphase
Nature
458
219-222
2009
Saccharomyces cerevisiae
Domecq, C.; Kireeva, M.; Archambault, J.; Kashlev, M.; Coulombe, B.; Burton, Z.F.
Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II
Protein Expr. Purif.
69
83-90
2010
Saccharomyces cerevisiae, Saccharomyces cerevisiae yBC-10
Feig, M.; Burton, Z.F.
RNA polymerase II flexibility during translocation from normal mode analysis
Proteins
78
434-446
2010
Saccharomyces cerevisiae
Kwapisz, M.; Beckouet, F.; Thuriaux, P.
Early evolution of eukaryotic DNA-dependent RNA polymerases
Trends Genet.
24
211-215
2008
Saccharomyces cerevisiae, Cenarchaeum symbiosum, Escherichia coli, Emiliania huxleyi, Methanocaldococcus jannaschii, Pyrococcus furiosus, Sulfolobus acidocaldarius, Saccharolobus solfataricus, Nanoarchaeum equitans, Caldivirga maquilingensis, Nitrosopumilus maritimus, Thermofilum pendens
Seibold, S.A.; Singh, B.N.; Zhang, C.; Kireeva, M.; Domecq, C.; Bouchard, A.; Nazione, A.M.; Feig, M.; Cukier, R.I.; Coulombe, B.; Kashlev, M.; Hampsey, M.; Burton, Z.F.
Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase
Biochim. Biophys. Acta
1799
575-587
2010
Saccharomyces cerevisiae, Thermus thermophilus
Arnold, J.J.; Smidansky, E.D.; Moustafa, I.M.; Cameron, C.E.
Human mitochondrial RNA polymerase: structure-function, mechanism and inhibition
Biochim. Biophys. Acta
1819
948-960
2012
Saccharomyces cerevisiae, Homo sapiens
Morrill, S.A.; Exner, A.E.; Babokhov, M.; Reinfeld, B.I.; Fuchs, S.M.
DNA instability maintains the repeat length of the yeast RNA polymerase II C-terminal domain
J. Biol. Chem.
291
11540-11550
2016
Saccharomyces cerevisiae, Saccharomyces cerevisiae GRY3019
Ramachandran, A.; Nandakumar, D.; Deshpande, A.P.; Lucas, T.P.; R-Bhojappa, R.; Tang, G.Q.; Raney, K.; Yin, Y.W.; Patel, S.S.
The yeast mitochondrial RNA polymerase and transcription factor complex catalyzes efficient priming of DNA synthesis on single-stranded DNA
J. Biol. Chem.
291
16828-16839
2016
Saccharomyces cerevisiae
Merkl, P.; Perez-Fernandez, J.; Pilsl, M.; Reiter, A.; Williams, L.; Gerber, J.; Boehm, M.; Deutzmann, R.; Griesenbeck, J.; Milkereit, P.; Tschochner, H.
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
Mol. Cell. Biol.
34
3817-3827
2014
Saccharomyces cerevisiae, Saccharomyces cerevisiae y2423
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