2ZGY

PARM with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability

Popp, D.Narita, A.Oda, T.Fujisawa, T.Matsuo, H.Nitanai, Y.Iwasa, M.Maeda, K.Onishi, H.Maeda, Y.

(2008) Embo J. 27: 570-579

  • DOI: 10.1038/sj.emboj.7601978
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ParM is a prokaryotic actin homologue, which ensures even plasmid segregation before bacterial cell division. In vivo, ParM forms a labile filament bundle that is reminiscent of the more complex spindle formed by microtubules partitioning chromosomes ...

    ParM is a prokaryotic actin homologue, which ensures even plasmid segregation before bacterial cell division. In vivo, ParM forms a labile filament bundle that is reminiscent of the more complex spindle formed by microtubules partitioning chromosomes in eukaryotic cells. However, little is known about the underlying structural mechanism of DNA segregation by ParM filaments and the accompanying dynamic instability. Our biochemical, TIRF microscopy and high-pressure SAX observations indicate that polymerization and disintegration of ParM filaments is driven by GTP rather than ATP and that ParM acts as a GTP-driven molecular switch similar to a G protein. Image analysis of electron micrographs reveals that the ParM filament is a left-handed helix, opposed to the right-handed actin polymer. Nevertheless, the intersubunit contacts are similar to those of actin. Our atomic model of the ParM-GMPPNP filament, which also fits well to X-ray fibre diffraction patterns from oriented gels, can explain why after nucleotide release, large conformational changes of the protomer lead to a breakage of intra- and interstrand interactions, and thus to the observed disintegration of the ParM filament after DNA segregation.


    Organizational Affiliation

    ERATO Actin Filament Dynamics Project, RIKEN Harima Institute, Japan Science and Technology Corporation, Sayo, Hyogo, Japan. dpopp@spring8.or.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plasmid segregation protein parM
A, B
320Escherichia coliMutation(s): 0 
Gene Names: parM (stbA)
Find proteins for P11904 (Escherichia coli)
Go to UniProtKB:  P11904
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-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: 1.9 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 64.437α = 90.00
b = 64.437β = 90.00
c = 201.021γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
MOLREPphasing
HKL-2000data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance