1cvr

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "1cvr" [edit=sysop:move=sysop])
Current revision (04:26, 17 October 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1cvr.png|left|200px]]
 
-
{{STRUCTURE_1cvr| PDB=1cvr | SCENE= }}
+
==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 [https://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 [https://proteopedia.org/fgij/fg.htm?mol=1CVR FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1cvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cvr OCA], [https://pdbe.org/1cvr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cvr RCSB], [https://www.ebi.ac.uk/pdbsum/1cvr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cvr ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[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).
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cv/1cvr_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
 +
<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/main_output.php?pdb_ID=1cvr ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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 the Arg specific cysteine proteinase gingipain R (RGPB)===
+
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>
-
{{ABSTRACT_PUBMED_10523290}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1cvr" style="background-color:#fffaf0;"></div>
-
==About this Structure==
+
==See Also==
-
[[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].
+
*[[Proteinase 3D structures|Proteinase 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:010523290</ref><references group="xtra"/>
+
__TOC__
-
[[Category: Gingipain R]]
+
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Porphyromonas gingivalis]]
[[Category: Porphyromonas gingivalis]]
-
[[Category: Beisel, H G.]]
+
[[Category: Beisel H-G]]
-
[[Category: Eichinger, A.]]
+
[[Category: Eichinger A]]
-
[[Category: Caspase]]
+
-
[[Category: Cysteine proteinase]]
+
-
[[Category: Hydrolase-hydrolase inhibitor complex]]
+

Current revision

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

PDB ID 1cvr

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

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