6C8D

RNA-dGMP complex with Mg ion

Summary for 6C8D

• Entry DOI: 10.2210/pdb6c8d/pdb
• Descriptor: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3'), 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: rna, deoxyguanosine
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 10633.24

Authors

Zhang, W.,Szostak, J.W. (deposition date: 2018-01-24, release date: 2018-05-30, Last modification date: 2023-10-04)

Primary citation

Zhang, W.,Walton, T.,Li, L.,Szostak, J.W.
Crystallographic observation of nonenzymatic RNA primer extension.
Elife, 7:-, 2018

PubMed Abstract: The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of life. Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved crystallography. We soaked crystals of an RNA primer-template-dGMP complex with guanosine-5'-phosphoro-2-aminoimidazolide for increasing times. At early times we see the activated ribonucleotides bound to the template, followed by formation of the imidazolium-bridged dinucleotide intermediate. At later times, we see a new phosphodiester bond forming between the primer and the incoming nucleotide. The intermediate is pre-organized because of the constraints of base-pairing with the template and hydrogen bonding between the imidazole amino group and both flanking phosphates. Our results provide atomic-resolution insight into the mechanism of nonenzymatic primer extension, and set the stage for further structural dissection and optimization of the RNA copying process.

PubMed: 29851379
DOI: 10.7554/eLife.36422

Experimental method

X-RAY DIFFRACTION (1.92 Å)