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Combination of NMR methods to solve key structures of the pRN1 primase in complex with its substrates | Abstract
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Journal of Computational Methods in Molecular Design

Abstract

Combination of NMR methods to solve key structures of the pRN1 primase in complex with its substrates

Author(s): Julien Boudet

Primases are single-stranded DNA dependent polymerases that synthesize RNA/DNA primers during replication. A primase, a DNA polymerase and an helicase compose the replication machinery of the archaeal plasmid pRN11. The structure of the archaeal functional primase domain has been solved by X-ray crystallography2,3 and it revealed an heteromeric structure with a catalytic prim/ pol domain tethered to a novel helix bundle domain. We investigated the NMR structure of the functional pRN1 primase domain in complex with a single-stranded DNA template containing the GTG motif4. We showed that the catalytic prim/pol domain of this 38 kDa enzyme is not required for template binding. Intermolecular contacts detected exclusively between the helix bundle domain and the DNA led us to isolate specifically this structurally independent unit. Our results are compatible with a conformational switch between a template-bound open state and a closed active complex3,5,6. We used multiple NMR dataset to solve the solution structures of the helix bundle domain in complex with the single-stranded DNA template alone and upon cofactors addition. Affinity measurements validated our structural data demonstrating the importance of residues located in helices 10 and 12 for the interaction with the GTG motif and confirmed the specificity improvement observed upon cofactors binding. ??????????????