6IUB

Structure of Helicobacter pylori Soj protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.902 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of HpSoj-DNA complexes and the nucleoid-adaptor complex formation in chromosome segregation.

Chu, C.H.Yen, C.Y.Chen, B.W.Lin, M.G.Wang, L.H.Tang, K.Z.Hsiao, C.D.Sun, Y.J.

(2019) Nucleic Acids Res. 47: 2113-2129

  • DOI: 10.1093/nar/gky1251
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ParABS, an important DNA partitioning process in chromosome segregation, includes ParA (an ATPase), ParB (a parS binding protein) and parS (a centromere-like DNA). The homologous proteins of ParA and ParB in Helicobacter pylori are HpSoj and HpSpo0J, ...

    ParABS, an important DNA partitioning process in chromosome segregation, includes ParA (an ATPase), ParB (a parS binding protein) and parS (a centromere-like DNA). The homologous proteins of ParA and ParB in Helicobacter pylori are HpSoj and HpSpo0J, respectively. We analyzed the ATPase activity of HpSoj and found that it is enhanced by both DNA and HpSpo0J. Crystal structures of HpSoj and its DNA complexes revealed a typical ATPase fold and that it is dimeric. DNA binding by HpSoj is promoted by ATP. The HpSoj-ATP-DNA complex non-specifically binds DNA through a continuous basic binding patch formed by lysine residues, with a single DNA-binding site. This complex exhibits a DNA-binding adept state with an active ATP-bound conformation, whereas the HpSoj-ADP-DNA complex may represent a transient DNA-bound state. Based on structural comparisons, HpSoj exhibits a similar DNA binding surface to the bacterial ParA superfamily, but the archaeal ParA superfamily exhibits distinct non-specific DNA-binding via two DNA-binding sites. We detected the HpSpo0J-HpSoj-DNA complex by electron microscopy and show that this nucleoid-adaptor complex (NAC) is formed through HpSoj and HpSpo0J interaction and parS DNA binding. NAC formation is promoted by HpSoj participation and specific parS DNA facilitation.


    Organizational Affiliation

    Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan.,Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SpoOJ regulator (Soj)
A, B
276Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Find proteins for O25759 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O25759
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.902 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.142α = 90.00
b = 93.322β = 90.00
c = 110.892γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (Taiwan)Taiwan--

Revision History 

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-03-13
    Type: Data collection, Database references