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) 
  • R-Value Work: 
    0.275 (Depositor) 
  • R-Value Observed: 
    0.275 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8QB1

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 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.

Macromolecule Content 

  • Total Structure Weight: 60.5 kDa 
  • Atom Count: 4,653 
  • Modeled Residue Count: 518 
  • Deposited Residue Count: 528 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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) 
  • R-Value Work:  0.275 (Depositor) 
  • 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