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1cvr

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Revision as of 11:23, 24 August 2017

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

Structural highlights

1cvr is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Activity:	Gingipain R, with EC number 3.4.22.37
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).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Eichinger A, Beisel HG, Jacob U, Huber R, Medrano FJ, Banbula A, Potempa J, Travis J, Bode W. Crystal structure of gingipain R: an Arg-specific bacterial cysteine proteinase with a caspase-like fold. EMBO J. 1999 Oct 15;18(20):5453-62. PMID:10523290 doi:10.1093/emboj/18.20.5453

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1cvr"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)==
 <StructureSection load='1cvr' size='340' side='right' caption='[[1cvr]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1cvr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33277 Atcc 33277]. 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>
+<table><tr><td colspan='2'>[[1cvr]] is a 1 chain structure. 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>
 </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=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></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=1cvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cvr OCA], [http://pdbe.org/1cvr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cvr RCSB], [http://www.ebi.ac.uk/pdbsum/1cvr PDBsum]</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=1cvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cvr OCA], [http://pdbe.org/1cvr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cvr RCSB], [http://www.ebi.ac.uk/pdbsum/1cvr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1cvr ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 18: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</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].
+</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/main_output.php?pdb_ID=1cvr ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 33277]]
 [[Category: Gingipain R]]
 [[Category: Beisel, H G]]

1cvr

From Proteopedia

Revision as of 11:23, 24 August 2017

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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