2d5l: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(5 intermediate revisions by the same user not shown)
Line 1: Line 1:
==Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis==
==Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis==
<StructureSection load='2d5l' size='340' side='right' caption='[[2d5l]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='2d5l' size='340' side='right'caption='[[2d5l]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2d5l]] 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=2D5L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D5L FirstGlance]. <br>
<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>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><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]] 2.1&#8491;</td></tr>
<tr><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=837 Porphyromonas gingivalis])</td></tr>
<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>
<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=2d5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d5l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d5l RCSB], [http://www.ebi.ac.uk/pdbsum/2d5l PDBsum]</span></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=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>
<table>
</table>
== Function ==
[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/d5/2d5l_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d5/2d5l_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>
   </jmolCheckbox>
   </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=2d5l ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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<ref>PMID:16914159</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
Line 32: Line 27:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Porphyromonas gingivalis]]
[[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]]

Latest revision as of 16:46, 13 March 2024

Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalisCrystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis

Structural highlights

2d5l is a 1 chain structure with sequence from Porphyromonas gingivalis W83. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

See Also

References

  1. ↑ 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

2d5l, resolution 2.10Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2d5l&oldid=4088650"