1nu8: Difference between revisions

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-[[Image:1nu8.png|left|200px]]
-<!--
+==Crystal structure of human dipeptidyl peptidase IV (DPP-IV) in complex with Diprotin A (IPI)==
-The line below this paragraph, containing "STRUCTURE_1nu8", creates the "Structure Box" on the page.
+<StructureSection load='1nu8' size='340' side='right'caption='[[1nu8]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1nu8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NU8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NU8 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-{{STRUCTURE_1nu8|  PDB=1nu8  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nu8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nu8 OCA], [https://pdbe.org/1nu8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nu8 RCSB], [https://www.ebi.ac.uk/pdbsum/1nu8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nu8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPP4_HUMAN DPP4_HUMAN] Cell surface glycoprotein receptor involved in the costimulatory signal essential for T-cell receptor (TCR)-mediated T-cell activation. Acts as a positive regulator of T-cell coactivation, by binding at least ADA, CAV1, IGF2R, and PTPRC. Its binding to CAV1 and CARD11 induces T-cell proliferation and NF-kappa-B activation in a T-cell receptor/CD3-dependent manner. Its interaction with ADA also regulates lymphocyte-epithelial cell adhesion. In association with FAP is involved in the pericellular proteolysis of the extracellular matrix (ECM), the migration and invasion of endothelial cells into the ECM. May be involved in the promotion of lymphatic endothelial cells adhesion, migration and tube formation. When overexpressed, enhanced cell proliferation, a process inhibited by GPC3. Acts also as a serine exopeptidase with a dipeptidyl peptidase activity that regulates various physiological processes by cleaving peptides in the circulation, including many chemokines, mitogenic growth factors, neuropeptides and peptide hormones. Removes N-terminal dipeptides sequentially from polypeptides having unsubstituted N-termini provided that the penultimate residue is proline.<ref>PMID:10951221</ref> <ref>PMID:17549790</ref> <ref>PMID:10570924</ref> <ref>PMID:10900005</ref> <ref>PMID:11772392</ref> <ref>PMID:14691230</ref> <ref>PMID:16651416</ref> <ref>PMID:17287217</ref> <ref>PMID:18708048</ref>
+== 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/nu/1nu8_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=1nu8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Inhibition of dipeptidyl peptidase IV (DPP-IV), the main glucagon-like peptide 1 (GLP1)-degrading enzyme, has been proposed for the treatment of type II diabetes. We expressed and purified the ectodomain of human DPP-IV in Pichia pastoris and determined the X-ray structure at 2.1 A resolution. The enzyme consists of two domains, the catalytic domain, with an alpha/beta hydrolase fold, and a beta propeller domain with an 8-fold repeat of a four-strand beta sheet motif. The beta propeller domain contributes two important functions to the molecule that have not been reported for such structures, an extra beta sheet motif that forms part of the dimerization interface and an additional short helix with a double Glu sequence motif. The Glu motif provides recognition and a binding site for the N terminus of the substrates, as revealed by the complex structure with diprotin A, a substrate with low turnover that is trapped in the tetrahedral intermediate of the reaction in the crystal.
-===Crystal structure of human dipeptidyl peptidase IV (DPP-IV) in complex with Diprotin A (ILI)===
+Structural basis of proline-specific exopeptidase activity as observed in human dipeptidyl peptidase-IV.,Thoma R, Loffler B, Stihle M, Huber W, Ruf A, Hennig M Structure. 2003 Aug;11(8):947-59. PMID:12906826<ref>PMID:12906826</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_12906826}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1nu8" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12906826 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_12906826}}
-==About this Structure==
-[[1nu8]] is a 3 chain structure of [[Dipeptidyl peptidase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NU8 OCA].
 ==See Also==
-*[[Dipeptidyl peptidase]]
+*[[Dipeptidyl peptidase 3D structures|Dipeptidyl peptidase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:12906826</ref><references group="xtra"/>
+__TOC__
-[[Category: Dipeptidyl-peptidase IV]]
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Hennig, M.]]
+[[Category: Large Structures]]
-[[Category: Huber, W.]]
+[[Category: Synthetic construct]]
-[[Category: Loeffler, B.]]
+[[Category: Hennig M]]
-[[Category: Ruf, A.]]
+[[Category: Huber W]]
-[[Category: Stihle, M.]]
+[[Category: Loeffler B]]
-[[Category: Thoma, R.]]
+[[Category: Ruf A]]
-[[Category: Alpha/beta hydrolase fold]]
+[[Category: Stihle M]]
-[[Category: B-barrel]]
+[[Category: Thoma R]]
-[[Category: Diprotin some]]
-[[Category: Exopeptidase]]