6DGD | pdb_00006dgd

PriA helicase bound to dsDNA of a DNA replication fork

• PDB DOI: https://doi.org/10.2210/pdb6DGD/pdb
• NAKB: 6DGD

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Klebsiella pneumoniae, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-17 Released: 2018-09-05 
• Deposition Author(s): Satyshur, K.A., Windgassen, T.A., Keck, J.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.82 Å
• R-Value Free: 
  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.250 (DCC) 

Starting Model: experimental

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

• PubMed: 30201718 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 183.64 kDa 
• Atom Count: 11,648 
• Modelled Residue Count: 1,454 
• Deposited Residue Count: 1,551 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Primosomal protein N'	A, B	751	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: priA, B1727_25905, CPT10_21250, SAMEA3304003_04572 EC: 3.6.4
UniProt
Find proteins for A6TGC5 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TGC5  Go to UniProtKB:  A6TGC5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')	C [auth W]	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*CP*GP*GP*CP*GP*TP*GP*CP*TP*C)-3')	D [auth X], F [auth Z]	12	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')	E [auth Y]	13	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	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	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 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.250 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.56	α = 90
b = 106.76	β = 90
c = 256.83	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-09-05 
Deposition Author(s): Satyshur, K.A., Windgassen, T.A., Keck, J.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM098885

Revision History  

• 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