9SMJ

Zuzalysin zymogen dodecahedral complex E439A

This is a non-PDB format compatible entry.

Summary for 9SMJ

• Entry DOI: 10.2210/pdb9smj/pdb
• Related: 9SLB 9SLL 9SLN 9SM4 9SM8
• EMDB information: 55005 55008 55026 55028 55035
• Descriptor: Zinc-dependent metalloprotease, CALCIUM ION, ZINC ION (3 entities in total)
• Functional Keywords: metallopeptidase, dodecahedral complex, zymogen, prophyromonas gingivalis, hydrolase
• Biological source: Porphyromonas gingivalis
• Total number of polymer chains: 60
• Total formula weight: 5834932.20

Authors

Rodriguez-Banqueri, A.,Madej, M.,Eckhard, U.,Potempa, J. (deposition date: 2025-09-08, release date: 2026-09-23)

Primary citation

Madej, M.,Rodriguez-Banqueri, A.,Mizgalska, D.,Szmigielski, B.,Nowakowska, Z.,Benedyk-Machaczka, M.,Bzowska, M.,Mikruta, K.,Ramirez-Larrota, J.S.,Agunanne, C.,Julien, O.,O'Donoghue, A.J.,Scavenius, C.,Lopez-Martin, M.,Marcos, E.,Koziej, L.,Glatt, S.,Guerra, P.,Eckhard, U.,Potempa, J.,Gomis-Ruth, F.X.
Structure and Function of a Multi-Megadalton Virus-Like Proteolytic Dodecahedron.
Angew.Chem.Int.Ed.Engl., :e5597279-e5597279, 2026

PubMed Abstract: Natural pentamer dodecahedra (Ddhs) span six orders of magnitude in diameter. Among proteins, only two catalytic Ddhs have been structurally characterized: lumazine synthase (LS) and the core of pyruvate dehydrogenase (PDH). Zuzalysin (ZUZ) is a ≈95-kDa metallopeptidase secreted for virulence by Porphyromonas gingivalis. Calcium converts latent flexible monomers into active ≈0.5-MDa pentamers that further assemble hierarchically into bipentamers, tripentamers, and a ≈5.6-MDa, ≈355-Å virus-like dodecahedron (Ddh). Experimental structures (1.8-3.6 Å) across these states reveal the molecular basis of activation, association, and catalysis, culminating in Ddh, which is physiologic, exceeds small viral capsids, and has 20 main entry pores and 60 lumen-facing active sites. ZUZ represents the largest catalytic protein assembly resolved at high resolution, exceeding LS, PDH, and major peptidase complexes in size and/or resolution.

PubMed: 42723362
DOI: 10.1002/anie.5597279

Experimental method

ELECTRON MICROSCOPY (2.64 Å)