1cvr

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{{STRUCTURE_1cvr| PDB=1cvr | SCENE= }}
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==Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)==
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===Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)===
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<StructureSection load='1cvr' size='340' side='right' caption='[[1cvr]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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{{ABSTRACT_PUBMED_10523290}}
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1cvr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Porphyromonas_gingivalis Porphyromonas gingivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CVR FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=H37:D-PHENYLALANYL-N-[(3S)-6-CARBAMIMIDAMIDO-1-CHLORO-2-OXOHEXAN-3-YL]-L-PHENYLALANINAMIDE'>H37</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
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<tr><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>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1cvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cvr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1cvr RCSB], [http://www.ebi.ac.uk/pdbsum/1cvr PDBsum]</span></td></tr>
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<table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cv/1cvr_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Gingipains are cysteine proteinases acting as key virulence factors of the bacterium Porphyromonas gingivalis, the major pathogen in periodontal disease. The 1.5 and 2.0 A crystal structures of free and D-Phe-Phe-Arg-chloromethylketone-inhibited gingipain R reveal a 435-residue, single-polypeptide chain organized into a catalytic and an immunoglobulin-like domain. The catalytic domain is subdivided into two subdomains comprising four- and six-stranded beta-sheets sandwiched by alpha-helices. Each subdomain bears topological similarities to the p20-p10 heterodimer of caspase-1. The second subdomain harbours the Cys-His catalytic diad and a nearby Glu arranged around the S1 specificity pocket, which carries an Asp residue to enforce preference for Arg-P1 residues. This gingipain R structure is an excellent template for the rational design of drugs with a potential to cure and prevent periodontitis. Here we show the binding mode of an arginine-containing inhibitor in the active-site, thus identifying major interaction sites defining a suitable pharmacophor.
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==Function==
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Crystal structure of gingipain R: an Arg-specific bacterial cysteine proteinase with a caspase-like fold.,Eichinger A, Beisel HG, Jacob U, Huber R, Medrano FJ, Banbula A, Potempa J, Travis J, Bode W EMBO J. 1999 Oct 15;18(20):5453-62. PMID:10523290<ref>PMID:10523290</ref>
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[[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).
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[1cvr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Porphyromonas_gingivalis Porphyromonas gingivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CVR OCA].
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</div>
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:010523290</ref><references group="xtra"/><references/>
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__TOC__
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</StructureSection>
[[Category: Gingipain R]]
[[Category: Gingipain R]]
[[Category: Porphyromonas gingivalis]]
[[Category: Porphyromonas gingivalis]]

Revision as of 04:16, 3 October 2014

Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)

1cvr, resolution 2.00Å

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