6DGD image
Deposition Date 2018-05-17
Release Date 2018-09-05
Last Version Date 2023-10-11
Entry Detail
PDB ID:
6DGD
Keywords:
DNA BINDING PROTEIN/DNA
Title:
PriA helicase bound to dsDNA of a DNA replication fork
Biological Source:
Source Organism:
Klebsiella pneumoniae (Taxon ID: 573)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.82 Å
R-Value Free:
0.28
R-Value Work:
0.24
Space Group:
P 21 21 21
6DGD validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Primosomal protein N'
Chain IDs:A, B
Chain Length:751
Number of Molecules:2
Biological Source:Klebsiella pneumoniae
UniProt ID:A6TGC5
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')
Chain IDs:C (auth: W)
Chain Length:12
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*GP*TP*CP*GP*GP*CP*GP*TP*GP*CP*TP*C)-3')
Chain IDs:D (auth: X), F (auth: Z)
Chain Length:12
Number of Molecules:2
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*GP*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')
Chain IDs:E (auth: Y)
Chain Length:13
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
SO4
ZN
Primary Citation
Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase.
Proc. Natl. Acad. Sci. U.S.A. 115 E9075 E9084 (2018)
PMID: 30201718 DOI: 10.1073/pnas.1809842115

Abstact

DNA replication restart, the essential process that reinitiates prematurely terminated genome replication reactions, relies on exquisitely specific recognition of abandoned DNA replication-fork structures. The PriA DNA helicase mediates this process in bacteria through mechanisms that remain poorly defined. We report the crystal structure of a PriA/replication-fork complex, which resolves leading-strand duplex DNA bound to the protein. Interaction with PriA unpairs one end of the DNA and sequesters the 3'-most nucleotide from the nascent leading strand into a conserved protein pocket. Cross-linking studies reveal a surface on the winged-helix domain of PriA that binds to parental duplex DNA. Deleting the winged-helix domain alters PriA's structure-specific DNA unwinding properties and impairs its activity in vivo. Our observations lead to a model in which coordinated parental-, leading-, and lagging-strand DNA binding provide PriA with the structural specificity needed to act on abandoned DNA replication forks.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
6DCR
4NL4
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