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| | ==The Crystal Structure of S603A Mutated Prolyl Tripeptidyl Aminopeptidase Complexed with Substrate== | | ==The Crystal Structure of S603A Mutated Prolyl Tripeptidyl Aminopeptidase Complexed with Substrate== |
| - | <StructureSection load='2dcm' size='340' side='right' caption='[[2dcm]], [[Resolution|resolution]] 2.90Å' scene=''> | + | <StructureSection load='2dcm' size='340' side='right'caption='[[2dcm]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2dcm]] is a 1 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=2DCM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DCM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2dcm]] is a 1 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=2DCM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DCM FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GA0:GLYCYLALANYL-N-2-NAPHTHYL-L-PROLINEAMIDE'>GA0</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2d5l|2d5l]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GA0:GLYCYLALANYL-N-2-NAPHTHYL-L-PROLINEAMIDE'>GA0</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PG1361 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=242619 PORGI])</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=2dcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dcm OCA], [https://pdbe.org/2dcm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dcm RCSB], [https://www.ebi.ac.uk/pdbsum/2dcm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dcm ProSAT]</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=2dcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dcm OCA], [http://pdbe.org/2dcm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dcm RCSB], [http://www.ebi.ac.uk/pdbsum/2dcm PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PTP_PORGI PTP_PORGI]] Serine proteinase. Releases tripeptides from the free amino terminus of proteins. Has a requirement for Pro in the P1 position, but is inactivated by Pro in the P1' position.<ref>PMID:10092598</ref> | + | [https://www.uniprot.org/uniprot/PTP_PORGI PTP_PORGI] Serine proteinase. Releases tripeptides from the free amino terminus of proteins. Has a requirement for Pro in the P1 position, but is inactivated by Pro in the P1' position.<ref>PMID:10092598</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dc/2dcm_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dc/2dcm_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Porgi]] | + | [[Category: Large Structures]] |
| - | [[Category: Ito, K]] | + | [[Category: Porphyromonas gingivalis W83]] |
| - | [[Category: Nakajima, Y]] | + | [[Category: Ito K]] |
| - | [[Category: Onohara, Y]] | + | [[Category: Nakajima Y]] |
| - | [[Category: Xu, Y]] | + | [[Category: Onohara Y]] |
| - | [[Category: Yamada, N]] | + | [[Category: Xu Y]] |
| - | [[Category: Yoshimoto, T]] | + | [[Category: Yamada N]] |
| - | [[Category: Hydrolase]]
| + | [[Category: Yoshimoto T]] |
| - | [[Category: Peptidase family s9]]
| + | |
| - | [[Category: Prolyl oligopeptidase family]]
| + | |
| - | [[Category: Serine peptidase]]
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| - | [[Category: Site-directed mutangenesis]]
| + | |
| Structural highlights
Function
PTP_PORGI Serine proteinase. Releases tripeptides from the free amino terminus of proteins. Has a requirement for Pro in the P1 position, but is inactivated by Pro in the P1' position.[1]
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
The crystal structure of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis was determined. Prolyl tripeptidyl aminopeptidase consists of beta-propeller and catalytic domains, and a large cavity between the domains; this structure is similar to dipeptidyl aminopeptidase IV. A catalytic triad (Ser603, His710, and Asp678) was located in the catalytic domain; this triad was virtually identical to that of the enzymes belonging to the prolyl oligopeptidase family. The structure of an inactive S603A mutant enzyme complexed with a substrate was also determined. The pyrrolidine ring of the proline residue appeared to fit into a hydrophobic pocket composed of Tyr604, Val629, Trp632, Tyr635, Tyr639, Val680, and Val681. There were characteristic differences in the residues of the beta-propeller domain, and these differences were related to the substrate specificity of tripeptidyl activity. The N-terminal amino group was recognized by salt bridges, with two carboxyl groups of Glu205 and Glu206 from a helix in dipeptidyl aminopeptidase IV. In prolyl tripeptidyl aminopeptidase, however, the Glu205 (located in the loop) and Glu636 were found to carry out this function. The loop structure provides sufficient space to accommodate three N-terminal residues (Xaa-Xaa-Pro) of substrates. This is the first report of the structure and substrate recognition mechanism of tripeptidyl peptidase.
Crystal structure and mechanism of tripeptidyl activity of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis.,Ito K, Nakajima Y, Xu Y, Yamada N, Onohara Y, Ito T, Matsubara F, Kabashima T, Nakayama K, Yoshimoto T J Mol Biol. 2006 Sep 15;362(2):228-40. Epub 2006 Aug 17. PMID:16914159[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Banbula A, Mak P, Bugno M, Silberring J, Dubin A, Nelson D, Travis J, Potempa J. Prolyl tripeptidyl peptidase from Porphyromonas gingivalis. A novel enzyme with possible pathological implications for the development of periodontitis. J Biol Chem. 1999 Apr 2;274(14):9246-52. PMID:10092598
- ↑ Ito K, Nakajima Y, Xu Y, Yamada N, Onohara Y, Ito T, Matsubara F, Kabashima T, Nakayama K, Yoshimoto T. Crystal structure and mechanism of tripeptidyl activity of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis. J Mol Biol. 2006 Sep 15;362(2):228-40. Epub 2006 Aug 17. PMID:16914159 doi:http://dx.doi.org/10.1016/j.jmb.2006.06.083
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