6GVU image
Entry Detail
PDB ID:
6GVU
Keywords:
DNA BINDING PROTEIN
Title:
NMR structure of the DNA-bound helix bundle domain from the functional pRN1 primase
Biological Source:
Source Organism:
Sulfolobus islandicus
Host Organism:
Escherichia coli BL21(DE3)
PDB Version:
Deposition Date:
2018-06-21
Release Date:
2018-12-26
Method Details:
Experimental Method:
SOLUTION NMR
Conformers Calculated:
200
Conformers Submitted:
20
Selection Criteria:
structures with the lowest energy
6GVU validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')
Chain IDs:A
Chain Length:9
Number of Molecules:1
Biological Source:Sulfolobus islandicus
Protein Blast
Polymer Type:polypeptide(L)
Description:functional pRN1 primase
Chain IDs:B
Chain Length:115
Number of Molecules:1
Biological Source:Sulfolobus islandicus
UniProt ID:Q54324 Pfam ID:PF13010 EC:2.7.7.102
Ligand Molecules
NA
Primary Citation
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)
PMID: 30595448 DOI: 10.1016/j.cell.2018.11.031

Abstact

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.

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Primary Citation of related structures
6GVU