6i9a
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==Porphyromonas gingivalis gingipain K (Kgp) in complex with inhibitor KYT-36== | |
| + | <StructureSection load='6i9a' size='340' side='right'caption='[[6i9a]], [[Resolution|resolution]] 1.20Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6i9a]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I9A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I9A FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTV:(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL'>DTV</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H8E:benzyl-N-[(2S)-1-[[(3S)-7-amino-1-(benzylamino)-1,2-dioxoheptan-3-yl]amino]-5-(2-methyl-2-phenylhydrazinyl)-1,5-dioxopentan-2-yl]carbamate'>H8E</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6i9a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i9a OCA], [http://pdbe.org/6i9a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i9a RCSB], [http://www.ebi.ac.uk/pdbsum/6i9a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i9a ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == 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] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == 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<ref>PMID:28196869</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 6i9a" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Gingipain K]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Gomis-Ruth, F X]] | ||
| + | [[Category: Guevara, T]] | ||
| + | [[Category: Rofdriguez-Banqueri, A]] | ||
| + | [[Category: Custeine peptidase]] | ||
| + | [[Category: Gingipain]] | ||
| + | [[Category: Hydrolase]] | ||
| + | [[Category: Peptidase inhibitor]] | ||
| + | [[Category: Periodontal disease]] | ||
| + | [[Category: Periodontopathogen]] | ||
| + | [[Category: Porphyromonas gingivali]] | ||
Revision as of 12:03, 13 March 2019
Porphyromonas gingivalis gingipain K (Kgp) in complex with inhibitor KYT-36
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