5MUN

Structural insight into zymogenic latency of gingipain K from Porphyromonas gingivalis.

Summary for 5MUN

• Entry DOI: 10.2210/pdb5mun/pdb
• Descriptor: Lys-gingipain W83, AZIDE ION (3 entities in total)
• Functional Keywords: cysteine protease, zymogenic latency, hydrolase
• Biological source: Porphyromonas gingivalis
• Cellular location: Lys-gingipain catalytic subunit: Secreted, extracellular space . 39 kDa adhesin: Secreted, extracellular space . 15 kDa adhesin: Secreted, extracellular space . 44 kDa adhesin: Secreted, extracellular space : Q51817
• Total number of polymer chains: 2
• Total formula weight: 46892.88

Authors

Pomowski, A.,Uson, I.,Nowakovska, Z.,Veillard, F.,Sztukowska, M.N.,Guevara, T.,Goulas, T.,Mizgalska, D.,Nowak, M.,Potempa, B.,Huntington, J.A.,Potempa, J.,Gomis-Ruth, F.X. (deposition date: 2017-01-13, release date: 2017-02-22, Last modification date: 2024-05-08)

Primary citation

Pomowski, A.,Uson, I.,Nowakowska, Z.,Veillard, F.,Sztukowska, M.N.,Guevara, T.,Goulas, T.,Mizgalska, D.,Nowak, M.,Potempa, B.,Huntington, J.A.,Potempa, J.,Gomis-Ruth, F.X.
Structural insights unravel the zymogenic mechanism of the virulence factor gingipain K from Porphyromonas gingivalis, a causative agent of gum disease from the human oral microbiome.
J. Biol. Chem., 292:5724-5735, 2017

PubMed Abstract: Skewing of the human oral microbiome causes dysbiosis and preponderance of bacteria such as , the main etiological agent of periodontitis. secretes proteolytic gingipains (Kgp and RgpA/B) as zymogens inhibited by a pro-domain that is removed during extracellular activation. Unraveling the molecular mechanism of Kgp zymogenicity is essential to design inhibitors blocking its activity. Here, we found that the isolated 209-residue Kgp pro-domain is a boomerang-shaped all-β protein similar to the RgpB pro-domain. Using composite structural information of Kgp and RgpB, we derived a plausible homology model and mechanism of Kgp-regulating zymogenicity. Accordingly, the pro-domain would laterally attach to the catalytic moiety in Kgp and block the active site through an exposed inhibitory loop. This loop features a lysine (Lys) likely occupying the S specificity pocket and exerting latency. Lys mutation to glutamate or arginine led to misfolded protein that was degraded Mutation to alanine gave milder effects but still strongly diminished proteolytic activity, without affecting the subcellular location of the enzyme. Accordingly, the interactions of Lys within the S pocket are also essential for correct folding. Uniquely for gingipains, the isolated Kgp pro-domain dimerized through an interface, which partially overlapped with that between the catalytic moiety and the pro-domain within the zymogen, both complexes are mutually exclusive. Thus, pro-domain dimerization, together with partial rearrangement of the active site upon activation, explains the lack of inhibition of the pro-domain in Our results reveal that the specific latency mechanism of Kgp differs from those of Rgps.

PubMed: 28196869
DOI: 10.1074/jbc.M117.776724

Experimental method

X-RAY DIFFRACTION (1.8 Å)