2OZE | pdb_00002oze

The Crystal structure of Delta protein of pSM19035 from Streptoccocus pyogenes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 
    0.218 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.193 (DCC) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Streptococcus pyogenes pSM19035 requires dynamic assembly of ATP-bound ParA and ParB on parS DNA during plasmid segregation.

Pratto, F.Cicek, A.Weihofen, W.A.Lurz, R.Saenger, W.Alonso, J.C.

(2008) Nucleic Acids Res 36: 3676-3689

  • DOI: https://doi.org/10.1093/nar/gkn170
  • Primary Citation Related Structures: 
    2OZE

  • PubMed Abstract: 

    The accurate partitioning of Firmicute plasmid pSM19035 at cell division depends on ATP binding and hydrolysis by homodimeric ATPase delta(2) (ParA) and binding of omega(2) (ParB) to its cognate parS DNA. The 1.83 A resolution crystal structure of delta(2) in a complex with non-hydrolyzable ATPgammaS reveals a unique ParA dimer assembly that permits nucleotide exchange without requiring dissociation into monomers. In vitro, delta(2) had minimal ATPase activity in the absence of omega(2) and parS DNA. However, stoichiometric amounts of omega(2) and parS DNA stimulated the delta(2) ATPase activity and mediated plasmid pairing, whereas at high (4:1) omega(2) : delta(2) ratios, stimulation of the ATPase activity was reduced and delta(2) polymerized onto DNA. Stimulation of the delta(2) ATPase activity and its polymerization on DNA required ability of omega(2) to bind parS DNA and its N-terminus. In vivo experiments showed that delta(2) alone associated with the nucleoid, and in the presence of omega(2) and parS DNA, delta(2) oscillated between the nucleoid and the cell poles and formed spiral-like structures. Our studies indicate that the molar omega(2) : delta(2) ratio regulates the polymerization properties of (delta*ATP*Mg(2+))(2) on and depolymerization from parS DNA, thereby controlling the temporal and spatial segregation of pSM19035 before cell division.


  • Organizational Affiliation
    • Department of Microbial Biotechnology, National Centre of Biotechnology, CSIC, 28049 Madrid, Spain.

Macromolecule Content 

  • Total Structure Weight: 35.26 kDa 
  • Atom Count: 2,613 
  • Modeled Residue Count: 284 
  • Deposited Residue Count: 298 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Orf delta'298Streptococcus pyogenesMutation(s): 0 
Gene Names: delta
UniProt
Find proteins for Q57280 (Streptococcus pyogenes)
Explore Q57280 
Go to UniProtKB:  Q57280
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57280
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free:  0.218 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.968α = 90
b = 82.968β = 90
c = 233.998γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description