5AG8

CRYSTAL STRUCTURE OF A MUTANT (665I6H) OF THE C-TERMINAL DOMAIN OF RGPB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Outer-Membrane Export Signal of Porphyromonas Gingivalis Type Ix Secretion System (T9Ss) is a Conserved C-Terminal Beta-Sandwich Domain.

De Diego, I.Ksiazek, M.Mizgalska, D.Koneru, L.Golik, P.Szmigielski, B.Nowak, M.Nowakowska, Z.Potempa, B.Houston, J.A.Enghild, J.J.Thogersen, I.B.Gao, J.Kwan, A.H.Trewhella, J.Dubin, G.Gomis-Ruth, F.X.Nguyen, K.Potempa, J.

(2016) Sci.Rep. 6: 23123

  • DOI: 10.1038/srep23123
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the recently characterized Type IX Secretion System (T9SS), the conserved C-terminal domain (CTD) in secreted proteins functions as an outer membrane translocation signal for export of virulence factors to the cell surface in the Gram-negative Bac ...

    In the recently characterized Type IX Secretion System (T9SS), the conserved C-terminal domain (CTD) in secreted proteins functions as an outer membrane translocation signal for export of virulence factors to the cell surface in the Gram-negative Bacteroidetes phylum. In the periodontal pathogen Porphyromonas gingivalis, the CTD is cleaved off by PorU sortase in a sequence-independent manner, and anionic lipopolysaccharide (A-LPS) is attached to many translocated proteins, thus anchoring them to the bacterial surface. Here, we solved the atomic structure of the CTD of gingipain B (RgpB) from P. gingivalis, alone and together with a preceding immunoglobulin-superfamily domain (IgSF). The CTD was found to possess a typical Ig-like fold encompassing seven antiparallel β-strands organized in two β-sheets, packed into a β-sandwich structure that can spontaneously dimerise through C-terminal strand swapping. Small angle X-ray scattering (SAXS) revealed no fixed orientation of the CTD with respect to the IgSF. By introducing insertion or substitution of residues within the inter-domain linker in the native protein, we were able to show that despite the region being unstructured, it nevertheless is resistant to general proteolysis. These data suggest structural motifs located in the two adjacent Ig-like domains dictate the processing of CTDs by the T9SS secretion pathway.


    Organizational Affiliation

    Proteolysis Lab; Department of Structural Biology; "María de Maeztu" Unit of Excellence; Molecular Biology Institute of Barcelona, CSIC; Barcelona Science Park, Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GINGIPAIN R2
A, B
168Porphyromonas gingivalis (strain ATCC BAA-308 / W83)Mutation(s): 0 
Gene Names: rgpB (prtRII, rgp2)
EC: 3.4.22.37
Find proteins for P95493 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Go to UniProtKB:  P95493
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.470α = 90.00
b = 61.740β = 117.79
c = 55.300γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release