8P6F

Crystal structure of PorX-Fj


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure-function analysis of PorX Fj , the PorX homolog from Flavobacterium johnsioniae, suggests a role of the CheY-like domain in type IX secretion motor activity.

Zammit, M.Bartoli, J.Kellenberger, C.Melani, P.Roussel, A.Cascales, E.Leone, P.

(2024) Sci Rep 14: 6577-6577

  • DOI: https://doi.org/10.1038/s41598-024-57089-9
  • Primary Citation of Related Structures:  
    8P6F

  • PubMed Abstract: 

    The type IX secretion system (T9SS) is a large multi-protein transenvelope complex distributed into the Bacteroidetes phylum and responsible for the secretion of proteins involved in pathogenesis, carbohydrate utilization or gliding motility. In Porphyromonas gingivalis, the two-component system PorY sensor and response regulator PorX participate to T9SS gene regulation. Here, we present the crystal structure of PorX Fj , the Flavobacterium johnsoniae PorX homolog. As for PorX, the PorX Fj structure is comprised of a CheY-like N-terminal domain and an alkaline phosphatase-like C-terminal domain separated by a three-helix bundle central domain. While not activated and monomeric in solution, PorX Fj crystallized as a dimer identical to active PorX. The CheY-like domain of PorX Fj is in an active-like conformation, and PorX Fj possesses phosphodiesterase activity, in agreement with the observation that the active site of its phosphatase-like domain is highly conserved with PorX.


  • Organizational Affiliation

    Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR7255), Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, Centre National de la Recherche Scientifique, Marseille, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Response regulator receiver domain-containing protein
A, B
540Flavobacterium johnsoniaeMutation(s): 0 
Gene Names: SAMN05444388_11078
UniProt
Find proteins for A0A1M5SPD1 (Flavobacterium johnsoniae)
Explore A0A1M5SPD1 
Go to UniProtKB:  A0A1M5SPD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1M5SPD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A]
J [auth B]
K [auth B]
L [auth B]
M [auth B]
F [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.609α = 90
b = 97.483β = 90
c = 131.103γ = 90
Software Package:
Software NamePurpose
autoBUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2024-04-03 
  • Deposition Author(s): Leone, P.

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-20-CE11-0011-01

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release