scholarly journals The active site of RNA polymerase II participates in transcript cleavage within arrested ternary complexes.

1994 ◽  
Vol 91 (17) ◽  
pp. 8057-8061 ◽  
Author(s):  
M. D. Rudd ◽  
M. G. Izban ◽  
D. S. Luse
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Active Site ◽  
Ternary Complexes ◽  
Transcript Cleavage

Characterization of the active site of yeast RNA polymerase II by DFT and ReaxFF calculations

2008 ◽  
Vol 120 (4-6) ◽  
pp. 479-489 ◽  
Author(s):  
Rui Zhu ◽  
Florian Janetzko ◽  
Yue Zhang ◽  
Adri C. T. van Duin ◽  
William A. Goddard ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Active Site

scholarly journals The Non-Coding B2 RNA Binds to the DNA Cleft and Active-Site Region of RNA Polymerase II

2013 ◽  
Vol 425 (19) ◽  
pp. 3625-3638 ◽  
Author(s):  
Steven L. Ponicsan ◽  
Stephane Houel ◽  
William M. Old ◽  
Natalie G. Ahn ◽  
James A. Goodrich ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Active Site ◽  
B2 Rna ◽  
Active Site Region

Comparative TFIIS-mediated transcript cleavage by mammalian RNA polymerase II arrested at a lesion in different transcription systems

DNA Repair ◽  
2005 ◽  
Vol 4 (10) ◽  
pp. 1075-1087 ◽  
Author(s):  
Virginia S. Kalogeraki ◽  
Silvia Tornaletti ◽  
Priscilla K. Cooper ◽  
Philip C. Hanawalt
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcript Cleavage

scholarly journals AT-rich sequence elements promote nascent transcript cleavage leading to RNA polymerase II termination

2012 ◽  
Vol 41 (3) ◽  
pp. 1797-1806 ◽  
Author(s):  
Eleanor White ◽  
Kinga Kamieniarz-Gdula ◽  
Michael J. Dye ◽  
Nick J. Proudfoot
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Nascent Transcript ◽  
Transcript Cleavage ◽  
Sequence Elements

NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases

2005 ◽  
Vol 83 (4) ◽  
pp. 486-496 ◽  
Author(s):  
Zachary F Burton ◽  
Michael Feig ◽  
Xue Q Gong ◽  
Chunfen Zhang ◽  
Yuri A Nedialkov ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Active Site ◽  
Binding Sites ◽  
Rna Synthesis ◽  
Rna Polymerases ◽  
Phosphoryl Transfer ◽  
Elongation Complex ◽  
Detailed Model ◽  
Loop 2

Multi-subunit RNA polymerases bind nucleotide triphosphate (NTP) substrates in the pretranslocated state and carry the dNMP–NTP base pair into the active site for phosphoryl transfer. NTP-driven translocation requires that NTP substrates enter the main-enzyme channel before loading into the active site. Based on this model, a new view of fidelity and efficiency of RNA synthesis is proposed. The model predicts that, during processive elongation, NTP-driven translocation is coupled to a protein conformational change that allows pyrophosphate release: coupling the end of one bond-addition cycle to substrate loading and translocation for the next. We present a detailed model of the RNA polymerase II elongation complex based on 2 low-affinity NTP binding sites located in the main-enzyme channel. This model posits that NTP substrates, elongation factors, and the conserved Rpb2 subunit fork loop 2 cooperate to regulate opening of the downstream transcription bubble.Key words: RNA polymerase, NTP-driven translocation, transcriptional fidelity, transcriptional efficiency, α-amanitin.

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