3HOW

Complete RNA polymerase II elongation complex III with a T-U mismatch and a frayed RNA 3'-uridine

Summary for 3HOW

• Entry DOI: 10.2210/pdb3how/pdb
• Related: 3HOU 3HOV 3HOX 3HOY 3HOZ
• 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: rna polymerase ii, metal-binding, transcription bubble, elongation complex, transcription, dna-rna mismatch, rna fraying, dna-binding, dna-directed rna polymerase, isopeptide bond, magnesium, nucleotidyltransferase, nucleus, phosphoprotein, transferase, ubl conjugation, zinc, zinc-finger, polymorphism, cytoplasm, dna damage, dna repair, mrna processing, transferase-dna-rna hybrid complex, transferase/dna/rna hybrid
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Cellular location: Nucleus: P04050 P38902 P08518 P16370 P20433 P20434 P34087 P20436 P27999; Nucleus, nucleolus: P22139 P40422; Cytoplasm: P20435
• Total number of polymer chains: 15
• Total formula weight: 535419.07

Authors

Sydow, J.F.,Brueckner, F.,Cheung, A.C.M.,Damsma, G.E.,Dengl, S.,Lehmann, E.,Vassylyev, D.,Cramer, P. (deposition date: 2009-06-03, release date: 2009-07-28, Last modification date: 2024-11-06)

Primary citation

Sydow, J.F.,Brueckner, F.,Cheung, A.C.M.,Damsma, G.E.,Dengl, S.,Lehmann, E.,Vassylyev, D.,Cramer, P.
Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
Mol.Cell, 34:710-721, 2009

PubMed Abstract: We show that RNA polymerase (Pol) II prevents erroneous transcription in vitro with different strategies that depend on the type of DNARNA base mismatch. Certain mismatches are efficiently formed but impair RNA extension. Other mismatches allow for RNA extension but are inefficiently formed and efficiently proofread by RNA cleavage. X-ray analysis reveals that a TU mismatch impairs RNA extension by forming a wobble base pair at the Pol II active center that dissociates the catalytic metal ion and misaligns the RNA 3' end. The mismatch can also stabilize a paused state of Pol II with a frayed RNA 3' nucleotide. The frayed nucleotide binds in the Pol II pore either parallel or perpendicular to the DNA-RNA hybrid axis (fraying sites I and II, respectively) and overlaps the nucleoside triphosphate (NTP) site, explaining how it halts transcription during proofreading, before backtracking and RNA cleavage.

PubMed: 19560423
DOI: 10.1016/j.molcel.2009.06.002

Experimental method

X-RAY DIFFRACTION (3.6 Å)