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Literature summary extracted from

  • 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 (2010), Biochim. Biophys. Acta, 1799, 575-587.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.7.7.6 recombinant Rpb2 R512C, TAP-tagged at the C-terminus of the RNAP II Rpb9 subunit Saccharomyces cerevisiae

Protein Variants

EC Number Protein Variants Comment Organism
2.7.7.6 E529A the substitution mutant is are faster than the wild-type enzyme in RNA elongation Saccharomyces cerevisiae
2.7.7.6 E529D the substitution mutant is are faster than the wild-type enzyme in RNA elongation Saccharomyces cerevisiae
2.7.7.6 E529Q the substitution mutant is are slower than the wild-type enzyme in RNA elongation Saccharomyces cerevisiae
2.7.7.6 additional information simulation of diverse McJ25-resistant mutations and their effects on enzyme activity, overview Thermus thermophilus
2.7.7.6 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 Thermus thermophilus
2.7.7.6 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 Saccharomyces cerevisiae
2.7.7.6 R766A the substitution is lethal, consistent with an important role for this invariant latch residue Saccharomyces cerevisiae
2.7.7.6 R766Q the substitution is lethal, consistent with an important role for this invariant latch residue Saccharomyces cerevisiae

Inhibitors

EC Number Inhibitors Comment Organism Structure
2.7.7.6 alpha-Amanitin the potent Sc RNAP II inhibitor binds to a ternary elongation complex with an open wedged conformation of the trigger loop Saccharomyces cerevisiae
2.7.7.6 Streptolydigin the antibiotic binds to a Tt RNAP TEC with an open trigger loop Thermus thermophilus

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.7.7.6 Mg2+ required Thermus thermophilus
2.7.7.6 Mg2+ required Saccharomyces cerevisiae

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.7.7.6 ATP + RNAn Thermus thermophilus
-
 diphosphate + RNAn+1
-
 ?
2.7.7.6 ATP + RNAn Saccharomyces cerevisiae
-
 diphosphate + RNAn+1
-
 ?
2.7.7.6 CTP + RNAn Thermus thermophilus
-
 diphosphate + RNAn+1
-
 ?
2.7.7.6 CTP + RNAn Saccharomyces cerevisiae
-
 diphosphate + RNAn+1
-
 ?
2.7.7.6 GTP + RNAn Thermus thermophilus
-
 diphosphate + RNAn+1
-
 ?
2.7.7.6 GTP + RNAn Saccharomyces cerevisiae
-
 diphosphate + RNAn+1
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.7.7.6 Saccharomyces cerevisiae
-
 strains YZS84 and YDP19
-
2.7.7.6 Thermus thermophilus
-
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.7.7.6 ATP + RNAn
-
 Thermus thermophilus diphosphate + RNAn+1
-
 ?
2.7.7.6 ATP + RNAn
-
 Saccharomyces cerevisiae diphosphate + RNAn+1
-
 ?
2.7.7.6 CTP + RNAn
-
 Thermus thermophilus diphosphate + RNAn+1
-
 ?
2.7.7.6 CTP + RNAn
-
 Saccharomyces cerevisiae diphosphate + RNAn+1
-
 ?
2.7.7.6 GTP + RNAn
-
 Thermus thermophilus diphosphate + RNAn+1
-
 ?
2.7.7.6 GTP + RNAn
-
 Saccharomyces cerevisiae diphosphate + RNAn+1
-
 ?

Synonyms

EC Number Synonyms Comment Organism
2.7.7.6 multi-subunit RNA polymerase
-
 Thermus thermophilus
2.7.7.6 multi-subunit RNA polymerase
-
 Saccharomyces cerevisiae
2.7.7.6 RNAP
-
 Thermus thermophilus
2.7.7.6 RNAP II
-
 Saccharomyces cerevisiae

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.7.7.6 25
-
 assay at Thermus thermophilus
2.7.7.6 25
-
 assay at Saccharomyces cerevisiae

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.7.7.6 7.6
-
 assay at Thermus thermophilus
2.7.7.6 7.6
-
 assay at Saccharomyces cerevisiae

General Information

EC Number General Information Comment Organism
2.7.7.6 malfunction mutant Sc Rpb2 R512C is slow in elongation Saccharomyces cerevisiae
2.7.7.6 malfunction R428A RNAP is instable Thermus thermophilus
2.7.7.6 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 Saccharomyces cerevisiae
2.7.7.6 additional information modeling of Tt RNAP TEC containing a closed, catalytic trigger helix conformation. RNA polymerase in a catalytic conformation demonstrates that the active site dNMP-NTP base pair must be substantially dehydrated to support full active site closing and optimum conditions for phosphodiester bond synthesis. An active site latch assembly that includes a key trigger helix residue beta' H1242 and highly conserved active site residues beta E445 and R557 appears to help regulate active site hydration/dehydration. Molecular dynamics simulations, overview Thermus thermophilus