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- PDB-8bv3: Bacillus subtilis DnaA domain III structure -

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Basic information

Entry
Database: PDB / ID: 8bv3
TitleBacillus subtilis DnaA domain III structure
ComponentsChromosomal replication initiator protein DnaA
KeywordsCELL CYCLE / DnaA / DNA replication / DNA replication initiation / AAA+ superfamily / Initiator Clade
Function / homology
Function and homology information


regulation of DNA replication / DNA replication origin binding / DNA replication initiation / DNA replication / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
DnaA N-terminal domain / DnaA N-terminal domain / DnaA, N-terminal domain superfamily / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix / DnaA protein signature. / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like ...DnaA N-terminal domain / DnaA N-terminal domain / DnaA, N-terminal domain superfamily / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix / DnaA protein signature. / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / Trp repressor/replication initiator / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Chromosomal replication initiator protein DnaA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsPintar, S. / Hubbard, J.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other government United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: The bacterial replication origin BUS promotes nucleobase capture.
Authors: Simone Pelliciari / Salomé Bodet-Lefèvre / Stepan Fenyk / Daniel Stevens / Charles Winterhalter / Frederic D Schramm / Sara Pintar / Daniel R Burnham / George Merces / Tomas T Richardson / ...Authors: Simone Pelliciari / Salomé Bodet-Lefèvre / Stepan Fenyk / Daniel Stevens / Charles Winterhalter / Frederic D Schramm / Sara Pintar / Daniel R Burnham / George Merces / Tomas T Richardson / Yumiko Tashiro / Julia Hubbard / Hasan Yardimci / Aravindan Ilangovan / Heath Murray /
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 ...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 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).
History
DepositionDec 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromosomal replication initiator protein DnaA
B: Chromosomal replication initiator protein DnaA
C: Chromosomal replication initiator protein DnaA
D: Chromosomal replication initiator protein DnaA
E: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,33524
Polymers137,3315
Non-polymers3,00419
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16330 Å2
ΔGint-57 kcal/mol
Surface area49650 Å2
Unit cell
Length a, b, c (Å)81.578, 81.578, 223.196
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Chromosomal replication initiator protein DnaA


Mass: 27466.150 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: dnaA, dnaH, BSU00010 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: P05648
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 293.15 K / Method: evaporation
Details: Morpheus H3: 0.02 M DL-Glutamic acid monohydrate, 0.02 M DL-Alanine, 0.0 2M Glycine, 0.2M DL-Lysine monohydrochloride, 0.02M DL-Serine, 0.1 M Imidazole/ MES monohydrate pH 6.5, 20% v/v Glycerol, 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.38→74.399 Å / Num. obs: 56743 / % possible obs: 85.3 % / Redundancy: 9.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.06 / Rrim(I) all: 0.189 / Net I/σ(I): 10.1
Reflection shellResolution: 2.38→2.52 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.461 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2842 / CC1/2: 0.461 / Rpim(I) all: 0.599 / Rrim(I) all: 1.583 / % possible all: 27.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROC1.0.5 (20211020)data reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L8Q

1l8q


Resolution: 2.38→74.399 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 2720 4.8 %RANDOM
Rwork0.1907 ---
obs0.1931 54023 85.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.19 Å2 / Biso mean: 50.058 Å2 / Biso min: 19.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 2.38→74.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9365 0 169 122 9656
Biso mean--40.03 33.96 -
Num. residues----1175
LS refinement shellResolution: 2.381→2.443 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 24 -
Rwork0.293 492 -
all-516 -
obs--10.43 %

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