2bgn: Difference between revisions

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-{{Seed}}
-[[Image:2bgn.png|left|200px]]
-<!--
+==HIV-1 Tat protein derived N-terminal nonapeptide Trp2-Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26)==
-The line below this paragraph, containing "STRUCTURE_2bgn", creates the "Structure Box" on the page.
+<StructureSection load='2bgn' size='340' side='right'caption='[[2bgn]], [[Resolution|resolution]] 3.15&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'>[[2bgn]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus], [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BGN 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]] 3.15&#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=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2bgn|  PDB=2bgn  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bgn OCA], [https://pdbe.org/2bgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bgn RCSB], [https://www.ebi.ac.uk/pdbsum/2bgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bgn 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/bg/2bgn_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2bgn ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+CD26 or dipeptidyl-peptidase IV (DPPIV) is engaged in immune functions by co-stimulatory effects on activation and proliferation of T lymphocytes, binding to adenosine deaminase, and regulation of various chemokines and cytokines. DPPIV peptidase activity is inhibited by both Tat protein from human immunodeficiency virus (HIV)-1 and its N-terminal nonapeptide Tat-(1-9) with amino acid sequence MDPVDPNIE, suggesting that DPPIV mediates immunosuppressive effects of Tat protein. The 2.0- and 3.15-A resolution crystal structures of the binary complex between human DPPIV and nonapeptide Tat-(1-9) and the ternary complex between the variant MWPVDPNIE, called Trp(2)-Tat-(1-9), and DPPIV bound to adenosine deaminase show that Tat-(1-9) and Trp(2)-Tat-(1-9) are located in the active site of DPPIV. The interaction pattern of DPPIV with Trp(2)-Tat-(1-9) is tighter than that with Tat-(1-9), in agreement with inhibition constants (K(i)) of 2 x 10(-6) and 250 x 10(-6) m, respectively. Both peptides cannot be cleaved by DPPIV because the binding pockets of the N-terminal 2 residues are interchanged compared with natural substrates: the N-terminal methionine occupies the hydrophobic S1 pocket of DPPIV that normally accounts for substrate specificity by binding the penultimate residue. Because the N-terminal sequence of the thromboxane A2 receptor resembles the Trp(2)-Tat-(1-9) peptide, a possible interaction with DPPIV is postulated.
-===HIV-1 TAT PROTEIN DERIVED N-TERMINAL NONAPEPTIDE TRP2-TAT (1-9) BOUND TO THE ACTIVE SITE OF DIPEPTIDYL PEPTIDASE IV (CD26)===
+Crystal structures of HIV-1 Tat-derived nonapeptides Tat-(1-9) and Trp2-Tat-(1-9) bound to the active site of dipeptidyl-peptidase IV (CD26).,Weihofen WA, Liu J, Reutter W, Saenger W, Fan H J Biol Chem. 2005 Apr 15;280(15):14911-7. Epub 2005 Jan 28. PMID:15695814<ref>PMID:15695814</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2bgn" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15695814}}, adds the Publication Abstract to the page
+*[[Adenosine deaminase 3D structures|Adenosine deaminase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15695814 is the PubMed ID number.
+*[[Dipeptidyl peptidase 3D structures|Dipeptidyl peptidase 3D structures]]
--->
+*[[Tat protein|Tat protein]]
-{{ABSTRACT_PUBMED_15695814}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-BGN is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BGN OCA].
+</StructureSection>
-==Reference==
-Crystal structures of HIV-1 Tat-derived nonapeptides Tat-(1-9) and Trp2-Tat-(1-9) bound to the active site of dipeptidyl-peptidase IV (CD26)., Weihofen WA, Liu J, Reutter W, Saenger W, Fan H, J Biol Chem. 2005 Apr 15;280(15):14911-7. Epub 2005 Jan 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15695814 15695814]
 [[Category: Bos taurus]]
-[[Category: Dipeptidyl-peptidase IV]]
 [[Category: Homo sapiens]]
-[[Category: Protein complex]]
+[[Category: Human immunodeficiency virus 1]]
-[[Category: Fan, H.]]
+[[Category: Large Structures]]
-[[Category: Liu, J.]]
+[[Category: Fan H]]
-[[Category: Reutter, W.]]
+[[Category: Liu J]]
-[[Category: Saenger, W.]]
+[[Category: Reutter W]]
-[[Category: Weihofen, W A.]]
+[[Category: Saenger W]]
-[[Category: Ada]]
+[[Category: Weihofen WA]]
-[[Category: Adenosine deaminase]]
-[[Category: Alpha/beta-hydrolase fold]]
-[[Category: Aminopeptidase]]
-[[Category: Beta-propeller fold]]
-[[Category: Cd26]]
-[[Category: Dipetidyl peptidase iv]]
-[[Category: Dppiv]]
-[[Category: Hiv-1 tat protein]]
-[[Category: Protein-protein complex]]
-[[Category: Serine protease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 04:19:41 2008''