1tkr: Difference between revisions

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-[[Image:1tkr.png|left|200px]]
-{{STRUCTURE_1tkr|  PDB=1tkr  |  SCENE=  }}
+==Human Dipeptidyl Peptidase IV/CD26 inhibited with Diisopropyl FluoroPhosphate==
+<StructureSection load='1tkr' size='340' side='right'caption='[[1tkr]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1tkr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TKR 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]] 2.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DFP:DIISOPROPYL+PHOSPHONATE'>DFP</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</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=1tkr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkr OCA], [https://pdbe.org/1tkr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tkr RCSB], [https://www.ebi.ac.uk/pdbsum/1tkr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tkr 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/tk/1tkr_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=1tkr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Human dipeptidyl peptidase IV (DPP-IV) is a ubiquitously expressed type II transmembrane serine protease. It cleaves the penultimate positioned prolyl bonds at the N terminus of physiologically important peptides such as the incretin hormones glucagon-like peptide 1 and glucose-dependent insulinotropic peptide. In this study, we have characterized different active site mutants. The Y547F mutant as well as the catalytic triad mutants S630A, D708A, and H740L showed less than 1% wild type activity. X-ray crystal structure analysis of the Y547F mutant revealed no overall changes compared with wild type apoDPP-IV, except the ablation of the hydroxyl group of Tyr(547) and a water molecule positioned in close proximity to Tyr(547). To elucidate further the reaction mechanism, we determined the crystal structure of DPP-IV in complex with diisopropyl fluorophosphate, mimicking the tetrahedral intermediate. The kinetic and structural findings of the tyrosine residue are discussed in relation to the catalytic mechanism of DPP-IV and to the inhibitory mechanism of the 2-cyanopyrrolidine class of potent DPP-IV inhibitors, proposing an explanation for the specificity of this class of inhibitors for the S9b family among serine proteases.
-===Human Dipeptidyl Peptidase IV/CD26 inhibited with Diisopropyl FluoroPhosphate===
+Tyrosine 547 constitutes an essential part of the catalytic mechanism of dipeptidyl peptidase IV.,Bjelke JR, Christensen J, Branner S, Wagtmann N, Olsen C, Kanstrup AB, Rasmussen HB J Biol Chem. 2004 Aug 13;279(33):34691-7. Epub 2004 Jun 2. PMID:15175333<ref>PMID:15175333</ref>
-{{ABSTRACT_PUBMED_15175333}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1tkr" style="background-color:#fffaf0;"></div>
-[[1tkr]] is a 2 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=1TKR OCA].
 ==See Also==
-*[[Dipeptidyl peptidase|Dipeptidyl peptidase]]
+*[[Dipeptidyl peptidase 3D structures|Dipeptidyl peptidase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:015175333</ref><references group="xtra"/>
+__TOC__
-[[Category: Dipeptidyl-peptidase IV]]
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Bjelke, J R.]]
+[[Category: Large Structures]]
-[[Category: Branner, S.]]
+[[Category: Bjelke JR]]
-[[Category: Christensen, J.]]
+[[Category: Branner S]]
-[[Category: Kanstrup, A B.]]
+[[Category: Christensen J]]
-[[Category: Olsen, C.]]
+[[Category: Kanstrup AB]]
-[[Category: Rasmussen, H B.]]
+[[Category: Olsen C]]
-[[Category: Wagtmann, N.]]
+[[Category: Rasmussen HB]]
-[[Category: Alpha/beta hydrolase]]
+[[Category: Wagtmann N]]
-[[Category: Beta-propeller]]
-[[Category: Homodimer]]
-[[Category: Hydrolase]]