8RAY | pdb_00008ray

ParA in complex with ATP

• PDB DOI: https://doi.org/10.2210/pdb8RAY/pdb

• Classification: REPLICATION
• Organism(s): Myxococcus xanthus DK 1622
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-12-01 Released: 2025-03-26 
• Deposition Author(s): Mais, C.-N., Bange, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.200 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Molecular basis of ParA ATPase activation by the CTPase ParB during bacterial chromosome segregation.

Schnabel, L., Osorio-Valeriano, M., Perez-Borrajero, C., Steinchen, W., Mais, C.N., Simon, B., Hanssmann, J., Thamm, M., Hennig, J., Bange, G., Thanbichler, M.

(2025) Nat Commun 16: 8428-8428

• PubMed: 40998818 
• DOI: https://doi.org/10.1038/s41467-025-63976-0
• Primary Citation of Related Structures:  
  8RAY


• PubMed Abstract: 
  

  DNA segregation by bacterial ParABS systems is mediated by transient tethering interactions between nucleoid-bound dimers of the ATPase ParA and centromere (parS)-associated complexes of the clamp-forming CTPase ParB. The lifetime of these interactions is limited by the ParB-dependent activation of ParA ATPase activity. Here, we elucidate the functional interplay between ParA and ParB in the model bacterium Myxococcus xanthus. We demonstrate that the N-terminal ParA-binding motif of ParB associates with a conserved bipartite binding pocket at the ParA dimer interface, in a manner dependent on ParB clamp closure. Moreover, we show that ParB and non-specific DNA interact cooperatively with ParA and synergistically induce structural changes in its Walker A and Walker B motifs that correlate with the activation of ParA ATPase activity. These results advance our understanding of the mechanism underlying DNA transport by the ParABS system and may help to unravel the mode of action of related cargo-positioning systems.

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Organizational Affiliation: 
• Department of Biology, Marburg University, Marburg, Germany.
Department of Biology, Marburg University, Marburg, Germany. [e-mail].
Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. [e-mail].
Department of Cell Biology, Harvard Medical School, Boston, MA, USA. [e-mail].
Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
Department of Chemistry, Marburg University, Marburg, Germany.
Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA.
Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Bayreuth, Germany.
Max Planck Fellow Group Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Department of Biology, Marburg University, Marburg, Germany. [e-mail].
Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. [e-mail].
Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 57.14 kDa 
• Atom Count: 4,352 
• Modeled Residue Count: 507 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ParA family protein	A [auth B], B [auth A]	255	Myxococcus xanthus DK 1622	Mutation(s): 1  Gene Names: MXAN_7477
UniProt
Find proteins for Q1CVJ3 (Myxococcus xanthus (strain DK1622)) Explore Q1CVJ3  Go to UniProtKB:  Q1CVJ3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	D [auth B], F [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	C [auth B], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.200 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.74	α = 90
b = 85.78	β = 90
c = 97.28	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-26 
Deposition Author(s): Mais, C.-N., Bange, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-03-26
  Type: Initial release
  
• Version 1.1: 2025-04-02
  Changes: Database references
• Version 2.0: 2025-07-16
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2025-10-08
  Changes: Database references