8BV3

Bacillus subtilis DnaA domain III structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The bacterial replication origin BUS promotes nucleobase capture.

Pelliciari, S.Bodet-Lefevre, S.Fenyk, S.Stevens, D.Winterhalter, C.Schramm, F.D.Pintar, S.Burnham, D.R.Merces, G.Richardson, T.T.Tashiro, Y.Hubbard, J.Yardimci, H.Ilangovan, A.Murray, H.

(2023) Nat Commun 14: 8339-8339

  • DOI: https://doi.org/10.1038/s41467-023-43823-w
  • Primary Citation of Related Structures:  
    8BTG, 8BV3

  • PubMed Abstract: 

    Genome duplication is essential for the proliferation of cellular life and this process is generally initiated by dedicated replication proteins at chromosome origins. In bacteria, DNA replication is initiated by the ubiquitous DnaA protein, which assembles into an oligomeric complex at the chromosome origin (oriC) that engages both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) to promote DNA duplex opening. However, the mechanism of DnaA specifically opening a replication origin was unknown. Here we show that Bacillus subtilis DnaA ATP assembles into a continuous oligomer at the site of DNA melting, extending from a dsDNA anchor to engage a single DNA strand. Within this complex, two nucleobases of each ssDNA binding motif (DnaA-trio) are captured within a dinucleotide binding pocket created by adjacent DnaA proteins. These results provide a molecular basis for DnaA specifically engaging the conserved sequence elements within the bacterial chromosome origin basal unwinding system (BUS).


  • Organizational Affiliation

    Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosomal replication initiator protein DnaA
A, B, C, D, E
243Bacillus subtilisMutation(s): 0 
Gene Names: dnaAdnaHBSU00010
UniProt
Find proteins for P05648 (Bacillus subtilis (strain 168))
Explore P05648 
Go to UniProtKB:  P05648
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05648
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
M [auth C],
R [auth D],
V [auth E]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
K
Query on K

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
K [auth B]
N [auth C]
O [auth C]
G [auth A],
J [auth B],
K [auth B],
N [auth C],
O [auth C],
P [auth C],
S [auth D],
T [auth D],
W [auth E]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
Q [auth C],
U [auth D],
X [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.578α = 90
b = 81.578β = 90
c = 223.196γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Database references