6T66 | pdb_00006t66

Crystal structure of the Vibrio cholerae replicative helicase (DnaB) with GDP-AlF4

• PDB DOI: https://doi.org/10.2210/pdb6T66/pdb

• Classification: REPLICATION
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-17 Released: 2021-04-28 
• Deposition Author(s): Legrand, P., Quevillon-Cheruel, S., Li de la Sierra-Gallay, I., Walbott, H.
• Funding Organization(s): French Infrastructure for Integrated Structural Biology (FRISBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.90 Å
• R-Value Free: 
  0.276 (Depositor), 0.296 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.269 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Starting Model: experimental

Literature

Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase.

Marsin, S., Adam, Y., Cargemel, C., Andreani, J., Baconnais, S., Legrand, P., Li de la Sierra-Gallay, I., Humbert, A., Aumont-Nicaise, M., Velours, C., Ochsenbein, F., Durand, D., Le Cam, E., Walbott, H., Possoz, C., Quevillon-Cheruel, S., Ferat, J.L.

(2021) Nucleic Acids Res 49: 6569-6586

• PubMed: 34107018 
• DOI: https://doi.org/10.1093/nar/gkab463
• Primary Citation Related Structures: 
  6T66


• PubMed Abstract: 
  

  Replicative helicases are essential proteins that unwind DNA in front of replication forks. Their loading depends on accessory proteins and in bacteria, DnaC and DnaI are well characterized loaders. However, most bacteria do not express either of these two proteins. Instead, they are proposed to rely on DciA, an ancestral protein unrelated to DnaC/I. While the DciA structure from Vibrio cholerae shares no homology with DnaC, it reveals similarities with DnaA and DnaX, two proteins involved during replication initiation. As other bacterial replicative helicases, VcDnaB adopts a toroid-shaped homo-hexameric structure, but with a slightly open dynamic conformation in the free state. We show that VcDnaB can load itself on DNA in vitro and that VcDciA stimulates this function, resulting in an increased DNA unwinding. VcDciA interacts with VcDnaB with a 3/6 stoichiometry and we show that a determinant residue, which discriminates DciA- and DnaC/I-helicases, is critical in vivo. Our work is the first step toward the understanding of the ancestral mode of loading of bacterial replicative helicases on DNA. It sheds light on the strategy employed by phage helicase loaders to hijack bacterial replicative helicases and may explain the recurrent domestication of dnaC/I through evolution in bacteria.

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Organizational Affiliation: 
• Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy 114 rue Edouard Vaillant, 94805 Villejuif, France.
Synchrotron SOLEIL, L'Orme des Merisiers, 91192 Gif-sur-Yvette, France.
Université de Versailles Saint Quentin, 45 avenue des Etats Unis, 78000 Versailles, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 321.05 kDa 
• Atom Count: 20,822 
• Modeled Residue Count: 2,644 
• Deposited Residue Count: 2,844 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicative DNA helicase	A, B, C, D, E, F	474	Vibrio cholerae	Mutation(s): 0  Gene Names: dnaB, BC353_11625, C9J66_17780, ERS013165_03687, ERS013200_03939, ERS013206_03692, F0315_03560, FLM02_14585, HPY05_12185 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.3 (UniProt)
UniProt
Find proteins for Q9KUY7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KUY7  Go to UniProtKB:  Q9KUY7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	G [auth A], J [auth B], M [auth C], P [auth D], S [auth E], V [auth F]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
ALF (Subject of Investigation/LOI)	I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	TETRAFLUOROALUMINATE ION Al F4 UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG (Subject of Investigation/LOI)	H [auth A], K [auth B], N [auth C], Q [auth D], T [auth E], W [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.90 Å
• R-Value Free:  0.276 (Depositor), 0.296 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.269 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.978	α = 90
b = 123.292	β = 90
c = 263.493	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-04-28 
Deposition Author(s): Legrand, P., Quevillon-Cheruel, S., Li de la Sierra-Gallay, I., Walbott, H.

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Funding Organization	Location	Grant Number
French Infrastructure for Integrated Structural Biology (FRISBI)	France	ANR-10-INBS-05

Revision History  

• Version 1.0: 2021-04-28
  Type: Initial release
  
• Version 1.1: 2021-06-23
  Changes: Database references
• Version 1.2: 2021-06-30
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description