2d5l

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[[Image:2d5l.gif|left|200px]]<br /><applet load="2d5l" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2d5l, resolution 2.10&Aring;" />
 
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'''Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis'''<br />
 
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==Overview==
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==Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis==
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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.
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<StructureSection load='2d5l' size='340' side='right'caption='[[2d5l]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2d5l]] 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=2D5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D5L FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d5l OCA], [https://pdbe.org/2d5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d5l RCSB], [https://www.ebi.ac.uk/pdbsum/2d5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d5l ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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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/d5/2d5l_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/main_output.php?pdb_ID=2d5l ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2D5L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Porphyromonas_gingivalis Porphyromonas gingivalis] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D5L OCA].
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*[[Tripeptidyl peptidase|Tripeptidyl peptidase]]
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== References ==
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==Reference==
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<references/>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16914159 16914159]
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__TOC__
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[[Category: Porphyromonas gingivalis]]
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</StructureSection>
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Ito, K.]]
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[[Category: Porphyromonas gingivalis W83]]
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[[Category: Nakajima, Y.]]
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[[Category: Ito K]]
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[[Category: Onohara, Y.]]
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[[Category: Nakajima Y]]
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[[Category: Xu, Y.]]
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[[Category: Onohara Y]]
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[[Category: Yamada, N.]]
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[[Category: Xu Y]]
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[[Category: Yoshimoto, T.]]
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[[Category: Yamada N]]
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[[Category: SO4]]
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[[Category: Yoshimoto T]]
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[[Category: peptidase family s9]]
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[[Category: prolyl oligopeptidase family]]
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[[Category: serine peptidase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:55:37 2008''
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Current revision

Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis

PDB ID 2d5l

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