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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

Reaction

nucleoside triphosphate
+
RNAn
=
diphosphate
 +
RNAn+1

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 Transferases
         2.7 Transferring phosphorus-containing groups
             2.7.7 Nucleotidyltransferases
                2.7.7.6 DNA-directed RNA polymerase

Engineering

Engineering on EC 2.7.7.6 - DNA-directed RNA polymerase

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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C70A/C72H/C85A/C88H
-
mutant enzyme is defective in intrinsic termination and antitermination in vitro. Mutation likely causes a recessive-lethal phenotype
C70H
-
mutant enzyme terminates more poorly than wild-type enzyme on put(-) templates, and responds weakly on put. Mutation likely causes a recessive-lethal phenotype
C72H
-
mutant enzyme terminates more poorly than wild-type enzyme on put(-) templates, and responds weakly on put. Mutation likely causes a recessive-lethal phenotype
C85H
-
mutant enzyme terminates more poorly than wild-type enzyme on put(-) templates, and responds weakly on put. Mutation likely causes a recessive-lethal phenotype
del70-88insGGGG
-
mutant enzyme terminates more poorly than wild-type enzyme on put(-) templates, and responds weakly on put. Mutation likely causes a recessive-lethal phenotype
del74-84insGGGG
-
mutant enzyme terminates more poorly than wild-type enzyme on put(-) templates, and responds weakly on put. Mutation likely causes a recessive-lethal phenotype
E813A/D814A
-
significantly decreased elongation rate, the mutation changes the effect of diphosphate on the 3'-5'-exonuclease reaction, whose addition stimulates the production of UMP through hydrolysis rather than of UTP through diphosphorolysis. The mutation makes the 3'-exonuclease activity independent of TTP. The mutation changes the response of TEC to diphosphate: instead of causing diphosphorolysis it stimulates the exonuclease reaction
N458A
-
significantly decreased elongation rate
R1106A
-
significantly decreased elongation rate, enhanced exonuclease activity
E244stop
-
random mutagenesis, identification of mutant L33, a truncated protein that lacks the C-terminal alpha-subunit, alphaCTD, but is capable of being assembled into the RNAP and carrying out transcription, while it does not respond to signals in the DNA or from protein effectors, overview. The mutant grows faster and exhibits a higher accumulated cell mass than the wild-type in the presence of butanol, phenotype, overview
V257F/L281P
-
random mutagenesis, the rpoA14 mutant shows mutations of the C-terminal alpha-subunit, phenotype, overview
V257R
-
random mutagenesis, the rpoA22 mutant shows a mutation of the C-terminal alpha-subunit, phenotype, overview
D421A
-
mutation results in an enzyme with reduced activity and altered patterns of transcription
D421T
-
mutation results in an enzyme with reduced activity and altered patterns of transcription
K631R
-
the fraction of catalytically active E form is 38% compared to 100% for the wild-type enzyme. The synthesis of long transcripts is markedly diminished for the mutant due to decreasing processivity
R423A
-
mutation results in an enzyme with reduced activity and altered patterns of transcription
R423K
-
mutation results in an enzyme with reduced activity and altered patterns of transcription
R425K
-
mutation results in an enzyme with reduced activity and altered patterns of transcription
S641A
-
mutation reduces activity in presence of Mg2+ to 93% of the activity of the wild-type enzyme
W422A
-
mutation results in an enzyme that has nearly normal levels of activity and exhibits patterns of transcription that are similar to that of the wild-type enzyme
W422F
-
mutation results in an enzyme that has nearly normal levels of activity and exhibits patterns of transcription that are similar to that of the wild-type enzyme
W422R
-
mutation results in an enzyme that has nearly normal levels of activity and exhibits patterns of transcription that are similar to that of the wild-type enzyme
W422S
-
mutation results in an enzyme that has nearly normal levels of activity and exhibitspatterns of transcription that arew similar to that of the wild-type enzyme
Y639/S641A
-
mutation reduces activity in presence of Mg2+ to 89% of the activity of the wild-type enzyme
Y639C
-
mutation reduces activity in presence of Mg2+ to 7.5% of the activity of the wild-type enzyme. The mutation reduces the catalytic specificity for ribonucleoside triphosphates versus deoxynucleoside triphosphates during transcript elongation, which is about 80 for the wild-type enzyme. The remaining specificity factor is 11
Y639F
Y639H
-
mutation reduces activity in presence of Mg2+ to 3.7% of the activity of the wild-type enzyme
Y639L
-
mutation reduces activity in presence of Mg2+ to 43% of the activity of the wild-type enzyme. The mutation reduces the catalytic specificity for ribonucleoside triphosphates versus deoxynucleoside triphosphates during transcript elongation, which is about 80 for the wild-type enzyme. The remaining specificity factor is 11
Y639M
-
mutation reduces activity in presence of Mg2+ to 50% of the activity of the wild-type enzyme. The mutation reduces the catalytic specificity for ribonucleoside triphosphates versus deoxynucleoside triphosphates during transcript elongation, which is about 80 for the wild-type enzyme. The remaining specificity factor is 5.5
Y639Q
-
mutation reduces activity in presence of Mg2+ to 1% of the activity of the wild-type enzyme. The mutation reduces the catalytic specificity for ribonucleoside triphosphates vs deoxynucleoside triphosphates during transcript elongation, which is about 80 for the wild-type enzyme. The remaining specificity factor is 4.5
Y639T
-
mutation reduces activity in presence of Mg2+ to 1.3% of the activity of the wild-type enzyme. The mutation reduces the catalytic specificity for ribonucleoside triphosphates versus deoxynucleoside triphosphates during transcript elongation, which is about 80 for the wild-type enzyme. The remaining specificity factor is 6.5
Y639V
-
mutation reduces activity in presence of Mg2+ to 4.3% of the activity of the wild-type enzyme. The mutation reduces the catalytic specificity for ribonucleoside triphosphates versus deoxynucleoside triphosphates during transcript elongation, which is about 80 for the wild-type enzyme. The remaining specificity factor is 19
G711K/N926S/N1103S/N1117S
-
site-directed mutagenesis, the mutant mitoRNAP that lacks four natural hydroxylamine cleavage sites
L640D
-
the mutant of the PA subunit shows reduced transcriptional activity compared to the wild-type enzyme
L666D
-
the mutant of the PA subunit shows reduced transcriptional activity compared to the wild-type enzyme
V636S
-
the mutant of the PA subunit shows reduced transcriptional activity compared to the wild-type enzyme
W706A
-
the mutant of the PA subunit shows reduced transcriptional activity compared to the wild-type enzyme
H426N
-
the rpoB(R)-specific missense mutation is essential for the activation of secondary metabolism, molecular mechanism, overview
R584A
-
site-directed mutagenesis, the RNAP holoenzyme containing this sigma70 mutant binds preferentially to promoters bearing a specifically mutated -35 element
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
K979Q
-
lethal mutation in subunit Rpb2
K979R
-
lethal mutation in subunit Rpb2
K987Q
-
lethal mutation in subunit Rpb2
K987R
-
lethal mutation in subunit Rpb2
Q513A
-
mutation in subunit Rpb2, the mutant shows a weak defect in the escape from a transcriptional stall at A20
R1020K
-
lethal mutation in subunit Rpb2
R1020Q
-
lethal mutation in subunit Rpb2
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
D505A
-
mutation in subunit Rpb2, the mutant shows a weak defect in the escape from a transcriptional stall at A20
-
E529A
-
mutation in subunit Rpb2, the mutant is faster in elongation compared to wild type RNAP II
-
E529D
-
mutation in subunit Rpb2, the mutant is faster in elongation compared to wild type RNAP II
-
R512C
-
mutation in subunit Rpb2, the mutant shows transcription elongation defects
-
R428A
-
site-directed mutagenesis, designed based on substitutions at the homologous position (Rpb2 R512) of Saccharomyces cerevisiae RNAP II, used as a reference structure, molecular dynamics simulations with starting Tt RNAP TEC structure, PDB 205J, that is in a strained, catalytic conformation that responds very sensitively to the R428A substitution but is stable for wild-type enzyme, overview. Long range conformational coupling linking a dynamic segment of the bridge alpha-helix, the extended fork loop, the active site, and the trigger loop-trigger helix is apparent and adversely affected in beta R428A RNAP. The R428A substitution is instable in the i+1 dTMP-ATP base pair, as indicated by fluctuations in the dTMP O4-ATP N6 base pairing distance in R428A
additional information