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| | <StructureSection load='5mun' size='340' side='right'caption='[[5mun]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='5mun' size='340' side='right'caption='[[5mun]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5mun]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MUN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5MUN FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5mun]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_gingivalis Porphyromonas gingivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MUN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MUN FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Gingipain_K Gingipain K], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.47 3.4.22.47] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5mun FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mun OCA], [http://pdbe.org/5mun PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mun RCSB], [http://www.ebi.ac.uk/pdbsum/5mun PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mun ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5mun FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mun OCA], [https://pdbe.org/5mun PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mun RCSB], [https://www.ebi.ac.uk/pdbsum/5mun PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mun ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KGP83_PORGN KGP83_PORGN]] Cysteine proteinase with a strong preference for substrates with Lys in the P1 position. Hydrolyzes bovine hemoglobin, bovine serum albumin, casein, human placental type I collagen and human IgA and IgG. Disrupts the functions of polymorphonuclear leukocytes. May act as a virulence factor in the development of peridontal disease. Involved in the coaggregation of P.gingivalis with other oral bacteria (By similarity).[UniProtKB:B2RLK2] | + | [https://www.uniprot.org/uniprot/KGP83_PORGN KGP83_PORGN] Cysteine proteinase with a strong preference for substrates with Lys in the P1 position. Hydrolyzes bovine hemoglobin, bovine serum albumin, casein, human placental type I collagen and human IgA and IgG. Disrupts the functions of polymorphonuclear leukocytes. May act as a virulence factor in the development of peridontal disease. Involved in the coaggregation of P.gingivalis with other oral bacteria (By similarity).[UniProtKB:B2RLK2] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Proteinase|Proteinase]] | |
| | *[[Proteinase 3D structures|Proteinase 3D structures]] | | *[[Proteinase 3D structures|Proteinase 3D structures]] |
| | == References == | | == References == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Gingipain K]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Gomis-Ruth, F X]] | + | [[Category: Porphyromonas gingivalis]] |
| - | [[Category: Goulas, T]] | + | [[Category: Gomis-Ruth FX]] |
| - | [[Category: Guevara, T]] | + | [[Category: Goulas T]] |
| - | [[Category: Huntington, J A]] | + | [[Category: Guevara T]] |
| - | [[Category: Mizgalska, D]] | + | [[Category: Huntington JA]] |
| - | [[Category: Nowak, M]] | + | [[Category: Mizgalska D]] |
| - | [[Category: Nowakovska, Z]] | + | [[Category: Nowak M]] |
| - | [[Category: Pomowski, A]] | + | [[Category: Nowakovska Z]] |
| - | [[Category: Potempa, B]] | + | [[Category: Pomowski A]] |
| - | [[Category: Potempa, J]] | + | [[Category: Potempa B]] |
| - | [[Category: Sztukowska, M N]] | + | [[Category: Potempa J]] |
| - | [[Category: Uson, I]] | + | [[Category: Sztukowska MN]] |
| - | [[Category: Veillard, F]] | + | [[Category: Uson I]] |
| - | [[Category: Cysteine protease]]
| + | [[Category: Veillard F]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Zymogenic latency]]
| + | |
| Structural highlights
Function
KGP83_PORGN Cysteine proteinase with a strong preference for substrates with Lys in the P1 position. Hydrolyzes bovine hemoglobin, bovine serum albumin, casein, human placental type I collagen and human IgA and IgG. Disrupts the functions of polymorphonuclear leukocytes. May act as a virulence factor in the development of peridontal disease. Involved in the coaggregation of P.gingivalis with other oral bacteria (By similarity).[UniProtKB:B2RLK2]
Publication Abstract from PubMed
Skewing of the human oral microbiome causes dysbiosis and preponderance of bacteria such as Porphyromonas gingivalis, the main etiological agent of periodontitis. P. gingivalis 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-beta 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 (K129) likely occupying the S1-specificity pocket and exerting latency. K129 mutation to glutamate or arginine led to misfolded protein that was degraded in vivo. Mutation to alanine gave milder effects but still strongly diminished proteolytic activity, without affecting the enzyme's subcellular location. Accordingly, the interactions of K129 within the S1 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, i.e. both complexes are mutually exclusive. Thus, pro-domain dimerization, together with partial rearrangement of the active site upon activation, explain the lack of inhibition of the pro-domain in trans. Our results reveal that the specific latency mechanism of Kgp differs from those of Rgps.
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.,Pomowski A, Uson I, Nowakowska ZM, Veillard F, Sztukowska MN, Guevara T, Goulas T, Mizgalska D, Nowak ML, Potempa BA, Huntington JA, Potempa J, Gomis-Ruth FX J Biol Chem. 2017 Feb 14. pii: jbc.M117.776724. doi: 10.1074/jbc.M117.776724. PMID:28196869[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Pomowski A, Uson I, Nowakowska ZM, Veillard F, Sztukowska MN, Guevara T, Goulas T, Mizgalska D, Nowak ML, Potempa BA, Huntington JA, Potempa J, Gomis-Ruth FX. 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. 2017 Feb 14. pii: jbc.M117.776724. doi: 10.1074/jbc.M117.776724. PMID:28196869 doi:http://dx.doi.org/10.1074/jbc.M117.776724
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