5HBY

RNA primer-template complex with 2-methylimidazole-activated monomer analogue-3 binding sites

Summary for 5HBY

• Entry DOI: 10.2210/pdb5hby/pdb
• Related: 5HBW 5HBX
• Descriptor: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*C)-3'), [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-(3-methyl-1~{H}-pyrazol-4-yl)phosphinic acid, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: rna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 5046.52

Authors

Zhang, W.,Tam, C.P.,Wang, J.,Szostak, J.W. (deposition date: 2016-01-03, release date: 2016-12-07, Last modification date: 2024-03-06)

Primary citation

Zhang, W.,Tam, C.P.,Wang, J.,Szostak, J.W.
Unusual Base-Pairing Interactions in Monomer-Template Complexes.
ACS Cent Sci, 2:916-926, 2016

PubMed Abstract: Many high-resolution crystal structures have contributed to our understanding of the reaction pathway for catalysis by DNA and RNA polymerases, but the structural basis of nonenzymatic template-directed RNA replication has not been studied in comparable detail. Here we present crystallographic studies of the binding of ribonucleotide monomers to RNA primer-template complexes, with the goal of improving our understanding of the mechanism of nonenzymatic RNA copying, and of catalysis by polymerases. To explore how activated ribonucleotides recognize and bind to RNA templates, we synthesized an unreactive phosphonate-linked pyrazole analogue of guanosine 5'-phosphoro-2-methylimidazolide (2-MeImpG), a highly activated nucleotide that has been used extensively to study nonenzymatic primer extension. We cocrystallized this analogue with structurally rigidified RNA primer-template complexes carrying single or multiple monomer binding sites, and obtained high-resolution X-ray structures of these complexes. In addition to Watson-Crick base pairing, we repeatedly observed noncanonical guanine:cytidine base pairs in our crystal structures. In most structures, the phosphate and leaving group moieties of the monomers were highly disordered, while in others the distance from O3' of the primer to the phosphorus of the incoming monomer was too great to allow for reaction. We suggest that these effects significantly influence the rate and fidelity of nonenzymatic RNA replication, and that even primitive ribozyme polymerases could enhance RNA replication by enforcing Watson-Crick base pairing between monomers and primer-template complexes, and by bringing the reactive functional groups into closer proximity.

PubMed: 28058281
DOI: 10.1021/acscentsci.6b00278

Experimental method

X-RAY DIFFRACTION (1.18 Å)