6ZA2

Crystal structure of dimeric latent PorU from Porphyromonas gingivalis

Summary for 6ZA2

• Entry DOI: 10.2210/pdb6za2/pdb
• Descriptor: Por secretion system protein porU, CALCIUM ION (3 entities in total)
• Functional Keywords: sortase, transpeptidase, type-ix secretion system, periodontopathogen, virulence factor, hydrolase
• Biological source: Porphyromonas gingivalis ATCC 33277
• Total number of polymer chains: 2
• Total formula weight: 256778.23

Authors

Gomis-Ruth, F.X.,Goulas, T.,Guevara, T.,Rodriguez-Banqueri, A.,Potempa, J.,Sola, M. (deposition date: 2020-06-04, release date: 2021-09-29, Last modification date: 2026-02-04)

Primary citation

Mizgalska, D.,Goulas, T.,Rodriguez-Banqueri, A.,Veillard, F.,Madej, M.,Malecka, E.,Szczesniak, K.,Ksiazek, M.,Widziolek, M.,Guevara, T.,Eckhard, U.,Sola, M.,Potempa, J.,Gomis-Ruth, F.X.
Intermolecular latency regulates the essential C-terminal signal peptidase and sortase of the Porphyromonas gingivalis type-IX secretion system.
Proc.Natl.Acad.Sci.USA, 118:-, 2021

PubMed Abstract: is a keystone pathogen of the human dysbiotic oral microbiome that causes severe periodontitis. It employs a type-IX secretion system (T9SS) to shuttle proteins across the outer membrane (OM) for virulence. Uniquely, T9SS cargoes carry a C-terminal domain (CTD) as a secretion signal, which is cleaved and replaced with anionic lipopolysaccharide by transpeptidation for extracellular anchorage to the OM. Both reactions are carried out by PorU, the only known dual-function, C-terminal signal peptidase and sortase. PorU is itself secreted by the T9SS, but its CTD is not removed; instead, intact PorU combines with PorQ, PorV, and PorZ in the OM-inserted "attachment complex." Herein, we revealed that PorU transits between active monomers and latent dimers and solved the crystal structure of the ∼260-kDa dimer. PorU has an elongated shape ∼130 Å in length and consists of seven domains. The first three form an intertwined N-terminal cluster likely engaged in substrate binding. They are followed by a gingipain-type catalytic domain (CD), two immunoglobulin-like domains (IGL), and the CTD. In the first IGL, a long "latency β-hairpin" protrudes ∼30 Å from the surface to form an intermolecular β-barrel with β-strands from the symmetric CD, which is in a latent conformation. Homology modeling of the competent CD followed by in vivo validation through a cohort of mutant strains revealed that PorU is transported and functions as a monomer through a C/H catalytic dyad. Thus, dimerization is an intermolecular mechanism for PorU regulation to prevent untimely activity until joining the attachment complex.

PubMed: 34593635
DOI: 10.1073/pnas.2103573118

Experimental method

X-RAY DIFFRACTION (3.35 Å)