6DGD

PriA helicase bound to dsDNA of a DNA replication fork

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.247 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase.

Windgassen, T.A., Leroux, M., Satyshur, K.A., Sandler, S.J., Keck, J.L.

(2018) Proc Natl Acad Sci U S A 115: E9075-E9084

  • DOI: https://doi.org/10.1073/pnas.1809842115
  • Primary Citation of Related Structures:  
    6DCR, 6DGD

  • PubMed Abstract: 

    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.

    • Organizational Affiliation: 

    Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Primosomal protein N'
A, B
751Klebsiella pneumoniaeMutation(s): 0 
Gene Names: priA, B1727_25905, CPT10_21250, SAMEA3304003_04572
EC: 3.6.4
UniProt
Find proteins for A0A1W2ITH4 (Klebsiella pneumoniae)
Explore A0A1W2ITH4 
Go to UniProtKB:  A0A1W2ITH4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1W2ITH4
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')C [auth W]12synthetic construct
Sequence Annotations
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*CP*GP*GP*CP*GP*TP*GP*CP*TP*C)-3')D [auth X],
F [auth Z]		12synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')E [auth Y]13synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
Q [auth B],
R [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.247 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.56α = 90
b = 106.76β = 90
c = 256.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM098885

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-09-19
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence, Structure summary
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description