6GVT

Hybrid structure of the pRN1 helix bundle domain in complex with DNA and 2 ATP molecules

Summary for 6GVT

• Entry DOI: 10.2210/pdb6gvt/pdb
• NMR Information: BMRB: 34290
• Descriptor: DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), functional pRN1 primase, ADENOSINE-5'-TRIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: prn1 primase, dinucleotide formation, quaternary structure of the helix bundle domain, synergistic effect, dna binding protein
• Biological source: Sulfolobus islandicus; More
• Total number of polymer chains: 2
• Total formula weight: 17298.49

Authors

Boudet, J.,Wiegand, T.,Meier, B.H.,Lipps, G.,Allain, F.H.-T. (deposition date: 2018-06-21, release date: 2018-12-26, Last modification date: 2019-08-21)

Primary citation

Boudet, J.,Devillier, J.C.,Wiegand, T.,Salmon, L.,Meier, B.H.,Lipps, G.,Allain, F.H.
A Small Helical Bundle Prepares Primer Synthesis by Binding Two Nucleotides that Enhance Sequence-Specific Recognition of the DNA Template.
Cell, 176:154-166.e13, 2019

PubMed Abstract: Primases have a fundamental role in DNA replication. They synthesize a primer that is then extended by DNA polymerases. Archaeoeukaryotic primases require for synthesis a catalytic and an accessory domain, the exact contribution of the latter being unresolved. For the pRN1 archaeal primase, this domain is a 115-amino acid helix bundle domain (HBD). Our structural investigations of this small HBD by liquid- and solid-state nuclear magnetic resonance (NMR) revealed that only the HBD binds the DNA template. DNA binding becomes sequence-specific after a major allosteric change in the HBD, triggered by the binding of two nucleotide triphosphates. The spatial proximity of the two nucleotides and the DNA template in the quaternary structure of the HBD strongly suggests that this small domain brings together the substrates to prepare the first catalytic step of primer synthesis. This efficient mechanism is likely general for all archaeoeukaryotic primases.

PubMed: 30595448
DOI: 10.1016/j.cell.2018.11.031

Experimental method

SOLID-STATE NMR
SOLUTION NMR