6DCR

E. coli PriA helicase winged helix domain deletion protein

PDB DOI: https://doi.org/10.2210/pdb6DCR/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-05-08 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.215
R-Value Work: 0.186
R-Value Observed: 0.187

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

PubMed: 30201718 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 155.6 kDa
Atom Count: 9,896
Modelled Residue Count: 1,239
Deposited Residue Count: 1,388
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Primosomal protein N'	A, B	694	Escherichia coli K-12	Mutation(s): 0 Gene Names: priA, b3935, JW3906 EC: 3.6.4
UniProt
Find proteins for P17888 (Escherichia coli (strain K12)) Explore P17888 Go to UniProtKB: P17888
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17888
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	C [auth A], D [auth A], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.215
R-Value Work: 0.186
R-Value Observed: 0.187
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.132	α = 90
b = 56.505	β = 97.67
c = 195.863	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-09-05

Deposition Author(s):

Satyshur, K.A.

Windgassen, T.A.

Keck, J.L.

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