3H3V

Yeast RNAP II containing poly(A)-signal sequence in the active site

Summary for 3H3V

• Entry DOI: 10.2210/pdb3h3v/pdb
• Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, ... (17 entities in total)
• Functional Keywords: transferase/dna/rna, dna-binding, phosphorylation, rna polymerase ii, metal-binding, nuclear protein, transcription bubble, elongation complex, transferase, transcription, polyadenylation, termination, dna-directed rna polymerase, isopeptide bond, magnesium, nucleotidyltransferase, nucleus, phosphoprotein, zinc-finger, dna damage, dna repair, mrna processing, transferase-dna-rna complex
• Biological source: Saccharomyces cerevisiae (yeast); More
• Cellular location: Nucleus: P04050 P38902 P08518 P16370 P20433 P20434 P34087 P20436; Nucleus, nucleolus : P22139 P40422 P27999; Cytoplasm : P20435
• Total number of polymer chains: 15
• Total formula weight: 531996.79

Authors

Dengl, S.,Cramer, P. (deposition date: 2009-04-17, release date: 2009-06-16, Last modification date: 2023-09-06)

Primary citation

Dengl, S.,Cramer, P.
Torpedo Nuclease Rat1 Is Insufficient to Terminate RNA Polymerase II in Vitro
J.Biol.Chem., 284:21270-21279, 2009

PubMed Abstract: Termination of RNA polymerase (pol) II transcription in vivo requires the 5'-RNA exonuclease Rat1. It was proposed that Rat1 degrades RNA from the 5'-end that is created by transcript cleavage, catches up with elongating pol II, and acts like a Torpedo that removes pol II from DNA. Here we test the Torpedo model in an in vitro system based on bead-coupled pol II elongation complexes (ECs). Recombinant Rat1 complexes with Rai1, and with Rai1 and Rtt103, degrade RNA extending from the EC until they reach the polymerase surface but fail to terminate pol II. Instead, the EC retains an approximately 18-nucleotide RNA that remains with its 3'-end at the active site and can be elongated. Thus, pol II termination apparently requires a factor or several factors in addition to Rat1, Rai1, and Rtt103, post-translational modifications of these factors, or unusual reaction conditions.

PubMed: 19535338
DOI: 10.1074/jbc.M109.013847

Experimental method

X-RAY DIFFRACTION (4 Å)