7Y7S

QDE-1 in complex with DNA template, RNA primer and AMPNPP

Summary for 7Y7S

• Entry DOI: 10.2210/pdb7y7s/pdb
• Descriptor: RNA-dependent RNA polymerase, DNA (5'-D(*GP*AP*AP*CP*TP*AP*TP*GP*GP*TP*CP*GP*GP*A)-3'), RNA (5'-R(*UP*CP*CP*GP*AP*CP*C)-3'), ... (8 entities in total)
• Functional Keywords: rna polymerase, qde-1, complex, ddrp, ampnpp, rna binding protein
• Biological source: Neurospora crassa; More
• Total number of polymer chains: 6
• Total formula weight: 248704.46

Authors

Cui, R.X.,Gan, J.H.,Ma, J.B. (deposition date: 2022-06-22, release date: 2022-09-28, Last modification date: 2023-11-29)

Primary citation

Cui, R.,Li, H.,Zhao, J.,Li, X.,Gan, J.,Ma, J.
Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1.
Nucleic Acids Res., 50:10169-10186, 2022

PubMed Abstract: Neurospora crassa protein QDE-1, a member of the two-barrel polymerase superfamily, possesses both DNA- and RNA-dependent RNA polymerase (DdRP and RdRP) activities. The dual activities are essential for the production of double-stranded RNAs (dsRNAs), the precursors of small interfering RNAs (siRNAs) in N. crassa. Here, we report five complex structures of N-terminal truncated QDE-1 (QDE-1ΔN), representing four different reaction states: DNA/RNA-templated elongation, the de novo initiation of RNA synthesis, the first step of nucleotide condensation during de novo initiation and initial NTP loading. The template strand is aligned by a bridge-helix and double-psi beta-barrels 2 (DPBB2), the RNA product is held by DPBB1 and the slab domain. The DNA template unpairs with the RNA product at position -7, but the RNA template remains paired. The NTP analog coordinates with cations and is precisely positioned at the addition site by a rigid trigger loop and a proline-containing loop in the active center. The unique C-terminal tail from the QDE-1 dimer partner inserts into the substrate-binding cleft and plays regulatory roles in RNA synthesis. Collectively, this work elucidates the conserved mechanisms for DNA/RNA-dependent dual activities by QDE-1 and other two-barrel polymerase superfamily members.

PubMed: 36039765
DOI: 10.1093/nar/gkac727

Experimental method

X-RAY DIFFRACTION (2.7 Å)