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| | <StructureSection load='4ief' size='340' side='right'caption='[[4ief]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='4ief' size='340' side='right'caption='[[4ief]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ief]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Porgi Porgi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IEF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ief]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_gingivalis_W83 Porphyromonas gingivalis W83]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IEF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></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=4ief FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ief OCA], [https://pdbe.org/4ief PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ief RCSB], [https://www.ebi.ac.uk/pdbsum/4ief PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ief ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PG_0506, prtRII, rgp2, rgpB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=242619 PORGI])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Gingipain_R Gingipain R], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.37 3.4.22.37] </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=4ief FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ief OCA], [http://pdbe.org/4ief PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ief RCSB], [http://www.ebi.ac.uk/pdbsum/4ief PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ief ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/CPG2_PORGI CPG2_PORGI]] Thiol protease which is believed to participate in intracellular degradation and turnover of proteins. Its proteolytic activity is a major factor in both periodontal tissue destruction and in bacterial host defense mechanisms. Activates complement C3 and C5 (By similarity). | + | [https://www.uniprot.org/uniprot/CPG2_PORGI CPG2_PORGI] Thiol protease which is believed to participate in intracellular degradation and turnover of proteins. Its proteolytic activity is a major factor in both periodontal tissue destruction and in bacterial host defense mechanisms. Activates complement C3 and C5 (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Gingipain R]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Porgi]] | + | [[Category: Porphyromonas gingivalis W83]] |
| - | [[Category: Diego, I de]]
| + | [[Category: Gomis-Ruth FX]] |
| - | [[Category: Gomis-Ruth, F X]] | + | [[Category: Guevara T]] |
| - | [[Category: Guevara, T]] | + | [[Category: Potempa B]] |
| - | [[Category: Potempa, B]] | + | [[Category: Potempa J]] |
| - | [[Category: Potempa, J]] | + | [[Category: Sztukowska M]] |
| - | [[Category: Sztukowska, M]] | + | [[Category: Veillard FT]] |
| - | [[Category: Veillard, F T]] | + | [[Category: De Diego I]] |
| - | [[Category: Alpha/beta/alpha sandwich]] | + | |
| - | [[Category: Cysteine endopeptidase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
4ief is a 8 chain structure with sequence from Porphyromonas gingivalis W83. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
CPG2_PORGI Thiol protease which is believed to participate in intracellular degradation and turnover of proteins. Its proteolytic activity is a major factor in both periodontal tissue destruction and in bacterial host defense mechanisms. Activates complement C3 and C5 (By similarity).
Publication Abstract from PubMed
Zymogenicity is a regulatory mechanism that prevents inadequate catalytic activity in the wrong context. It plays a central role in maintaining microbial virulence factors in an inactive form inside the pathogen until secretion. Among these virulence factors is the cysteine peptidase gingipain B (RgpB), which is the major virulence factor secreted by the periodontopathogen Porphyromonas gingivalis that attacks host vasculature and defense proteins. The structure of the complex between soluble mature RgpB, consisting of a catalytic domain and an immunoglobulin superfamily domain, and its 205-residue N-terminal prodomain, the largest structurally characterized to date for a cysteine peptidase, reveals a novel fold for the prodomain that is distantly related to sugar-binding lectins. It attaches laterally to the catalytic domain through a large concave surface. The main determinant for latency is a surface "inhibitory loop," which approaches the active-site cleft of the enzyme on its non-primed side in a substrate-like manner. It inserts an arginine (Arg(126)) into the S1 pocket, thus matching the substrate specificity of the enzyme. Downstream of Arg(126), the polypeptide leaves the cleft, thereby preventing cleavage. Moreover, the carbonyl group of Arg(126) establishes a very strong hydrogen bond with the co-catalytic histidine, His(440), pulling it away from the catalytic cysteine, Cys(473), and toward Glu(381), which probably plays a role in orienting the side chain of His(440) during catalysis. The present results provide the structural determinants of zymogenic inhibition of RgpB by way of a novel inhibitory mechanism for peptidases in general and open the field for the design of novel inhibitory strategies in the treatment of human periodontal disease.
Porphyromonas gingivalis Virulence Factor Gingipain RgpB Shows a Unique Zymogenic Mechanism for Cysteine Peptidases.,de Diego I, Veillard FT, Guevara T, Potempa B, Sztukowska M, Potempa J, Gomis-Ruth FX J Biol Chem. 2013 May 17;288(20):14287-96. doi: 10.1074/jbc.M112.444927. Epub, 2013 Apr 4. PMID:23558682[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ de Diego I, Veillard FT, Guevara T, Potempa B, Sztukowska M, Potempa J, Gomis-Ruth FX. Porphyromonas gingivalis Virulence Factor Gingipain RgpB Shows a Unique Zymogenic Mechanism for Cysteine Peptidases. J Biol Chem. 2013 May 17;288(20):14287-96. doi: 10.1074/jbc.M112.444927. Epub, 2013 Apr 4. PMID:23558682 doi:10.1074/jbc.M112.444927
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