2OZE

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 
  • R-Value Work: 0.192 

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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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
D [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.192 
  • 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