6TOP | pdb_00006top

Structure of the PorE C-terminal domain, a protein of T9SS from Porphyromonas gingivalis

PDB DOI: https://doi.org/10.2210/pdb6TOP/pdb
Entry: 6TOP supersedes: 6I9O

Classification: PROTEIN BINDING
Organism(s): Porphyromonas gingivalis JCVI SC001
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-12-11 Released: 2020-06-17
Deposition Author(s): Trinh, T.N., Cambillau, C., Roussel, A., Leone, P.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.215 (Depositor), 0.214 (DCC)
R-Value Work:
0.190 (Depositor), 0.189 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Type IX secretion system PorE C-terminal domain from Porphyromonas gingivalis in complex with a peptidoglycan fragment.

Trinh, N.T.T., Tran, H.Q., Van Dong, Q., Cambillau, C., Roussel, A., Leone, P.

(2020) Sci Rep 10: 7384-7384

PubMed: 32355178 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-020-64115-z
Primary Citation Related Structures:
6TOP

PubMed Abstract:
Porphyromonas gingivalis, the major human pathogen associated to periodontal diseases, utilizes the Bacteroidetes-specific type IX secretion system (T9SS) to export virulence factors. PorE is a periplasmic multi-domain lipoprotein associated to the outer membrane that was recently identified as essential for T9SS function. Little is known on T9SS at the structural level, and in particular its interaction with peptidoglycan. This prompted us to carry out structural studies on PorE full length as well as on its four isolated domains. Here we report the crystal structure of the C-terminal OmpA_C-like putative peptidoglycan-binding domain at 1.55 Å resolution. An electron density volume was identified in the protein cleft, making it possible to build a naturally-occurring peptidoglycan fragment. This result suggests that PorE interacts with peptidoglycan and that PorE could anchor T9SS to the cell wall.

Organizational Affiliation

Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France.

Macromolecule Content

Total Structure Weight: 72.53 kDa
Atom Count: 5,704
Modeled Residue Count: 604
Deposited Residue Count: 604
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OmpA family protein	A	154	Porphyromonas gingivalis JCVI SC001	Mutation(s): 0 Gene Names: A343_1565

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
OmpA family protein	B, C, D	150	Porphyromonas gingivalis JCVI SC001	Mutation(s): 0 Gene Names: A343_1565

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLD (Subject of Investigation/LOI) Query on MLD Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	GLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA C₃₇ H₅₉ N₇ O₂₀ UPFMKPIBAIPLHT-RSJSDIDPSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]