8P6F | pdb_00008p6f

Crystal structure of PorX-Fj


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.255 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

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 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
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