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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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 ...

    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; jlkeck@wisc.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Primosomal protein N'A, B751Klebsiella pneumoniaeMutation(s): 0 
Gene Names: 
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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')C [auth W]12synthetic construct
Protein Feature View
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Entity ID: 3
MoleculeChainsLengthOrganismImage
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
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*GP*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')E [auth Y]13synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / 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		 Ligand Interaction
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		 Ligand Interaction
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