8QB1 | pdb_00008qb1

C-terminal domain of mirolase from Tannerella forsythia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.302 (Depositor), 0.330 (DCC) 
  • R-Value Work: 
    0.275 (Depositor), 0.291 (DCC) 
  • R-Value Observed: 
    0.275 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and functional insights into the C-terminal signal domain of the Bacteroidetes type-IX secretion system.

Mizgalska, D.Rodriguez-Banqueri, A.Veillard, F.Ksiazek, M.Goulas, T.Guevara, T.Eckhard, U.Potempa, J.Gomis-Ruth, F.X.

(2024) Open Biol 14: 230448-230448

  • DOI: https://doi.org/10.1098/rsob.230448
  • Primary Citation of Related Structures:  
    8QB1

  • PubMed Abstract: 

    Gram-negative bacteria from the Bacteroidota phylum possess a type-IX secretion system (T9SS) for protein secretion, which requires cargoes to have a C-terminal domain (CTD). Structurally analysed CTDs are from Porphyromonas gingivalis proteins RgpB, HBP35, PorU and PorZ, which share a compact immunoglobulin-like antiparallel 3+4 β-sandwich (β1-β7). This architecture is essential as a P. gingivalis strain with a single-point mutant of RgpB disrupting the interaction of the CTD with its preceding domain prevented secretion of the protein. Next, we identified the C-terminus ('motif C-t.') and the loop connecting strands β3 and β4 ('motif Lβ3β4') as conserved. We generated two strains with insertion and replacement mutants of PorU, as well as three strains with ablation and point mutants of RgpB, which revealed both motifs to be relevant for T9SS function. Furthermore, we determined the crystal structure of the CTD of mirolase, a cargo of the Tannerella forsythia T9SS , which shares the same general topology as in Porphyromonas CTDs. However, motif Lβ3β4 was not conserved. Consistently, P. gingivalis could not properly secrete a chimaeric protein with the CTD of peptidylarginine deiminase replaced with this foreign CTD. Thus, the incompatibility of the CTDs between these species prevents potential interference between their T9SSs.


  • Organizational Affiliation

    Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mirolase
A, B, C, D, E
A, B, C, D, E, F
88Tannerella forsythiaMutation(s): 0 
UniProt
Find proteins for A0A0A7KVG3 (Tannerella forsythia)
Explore A0A0A7KVG3 
Go to UniProtKB:  A0A0A7KVG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A7KVG3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
M [auth C]
O [auth D]
R [auth E]
H [auth A],
K [auth B],
M [auth C],
O [auth D],
R [auth E],
T [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
J [auth B],
Q [auth E]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
L [auth C]
N [auth D]
P [auth E]
G [auth A],
I [auth B],
L [auth C],
N [auth D],
P [auth E],
S [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.302 (Depositor), 0.330 (DCC) 
  • R-Value Work:  0.275 (Depositor), 0.291 (DCC) 
  • R-Value Observed: 0.275 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.445α = 90
b = 81.445β = 90
c = 66.553γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Structure summary