9RTJ

Hydrid structure of the helix bundle domain of pRN1 primase in complex with DNA, ATP and dGTP

Summary for 9RTJ

• Entry DOI: 10.2210/pdb9rtj/pdb
• NMR Information: BMRB: 35007
• Descriptor: SF3 helicase domain-containing protein, DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: primase, hbd, dinucleotide, first base-pair, replication
• Biological source: Saccharolobus islandicus; More
• Total number of polymer chains: 2
• Total formula weight: 17624.89

Authors

Wu, P.,Damberger, F.F.,Zehnder, J.,Schroder, N.,Lipps, G.,Wiegand, T.,Allain, F.H.-T. (deposition date: 2025-07-02, release date: 2026-03-25, Last modification date: 2026-08-26)

Primary citation

Wu, P.,Damberger, F.F.,Zehnder, J.,Wehr, N.,Senning, N.,Lipps, G.,Wiegand, T.,Allain, F.H.
Structural and mechanistic insights into primer synthesis initiation by DNA primase.
Nat Commun, 17:-, 2026

PubMed Abstract: DNA primases synthesize short primers required for genome replication, yet the mechanism of initial dinucleotide formation remains poorly understood. Here, we investigate the primase encoded by the pRN1 plasmid from the thermoacidophile archaeon Sulfolobus islandicus, a minimal model for primer synthesis. Using nucleotide analogues to slow the reaction, we capture transient intermediates of dinucleotide formation. Structural NMR and modeling reveal that the ancillary domain simultaneously binds the DNA template and two initiating nucleotides. Unexpectedly, only the second nucleotide base-pairs with the template, whereas the first remains unpaired, inducing template-base flipping and linker interaction. This interaction promotes a closed conformation in which the second nucleotide moves from the initiation to the elongation site and the first forms a base pair in the initiation site, positioning both nucleotides for catalysis. These findings reveal a mechanism for template recognition, nucleotide assembly, and proofreading during primer initiation that is likely conserved among primases.

PubMed: 42399618
DOI: 10.1038/s41467-026-74862-8

Experimental method

SOLID-STATE NMR
SOLUTION NMR