1kuk: Difference between revisions

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-{{Seed}}
-[[Image:1kuk.png|left|200px]]
-<!--
+==Crystal Structure of a Taiwan Habu Venom Metalloproteinase complexed with pEKW.==
-The line below this paragraph, containing "STRUCTURE_1kuk", creates the "Structure Box" on the page.
+<StructureSection load='1kuk' size='340' side='right'caption='[[1kuk]], [[Resolution|resolution]] 1.45&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'>[[1kuk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Protobothrops_mucrosquamatus Protobothrops mucrosquamatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KUK 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]] 1.45&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
-{{STRUCTURE_1kuk|  PDB=1kuk  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kuk OCA], [https://pdbe.org/1kuk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kuk RCSB], [https://www.ebi.ac.uk/pdbsum/1kuk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kuk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VM2T3_PROMU VM2T3_PROMU] Snake venom metalloproteinase TM-3: fibrin(ogen)olytic protease which cleaves the Aalpha chain of fibrinogen (FGA) first followed by the Bbeta chain (FGB) and shows relatively low activity on the gamma chain (FGG).<ref>PMID:8068721</ref> <ref>PMID:8193588</ref>   Disintegrin trimucrin: inhibits platelet aggregation induced by ADP, thrombin, platelet-activating factor and collagen. Acts by inhibiting fibrinogen interaction with platelet receptors GPIIb/GPIIIa (ITGA2B/ITGB3).<ref>PMID:8068721</ref> <ref>PMID:8193588</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/ku/1kuk_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=1kuk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Venoms from crotalid and viperid snakes contain several peptide inhibitors which regulate the proteolytic activities of their snake-venom metalloproteinases (SVMPs) in a reversible manner under physiological conditions. In this report, we describe the high-resolution crystal structures of a SVMP, TM-3, from Taiwan habu (Trimeresurus mucrosquamatus) cocrystallized with the endogenous inhibitors pyroGlu-Asn-Trp (pENW), pyroGlu-Gln-Trp (pEQW) or pyroGlu-Lys-Trp (pEKW). The binding of inhibitors causes some of the residues around the inhibitor-binding environment of TM-3 to slightly move away from the active-site center, and displaces two metal-coordinated water molecules by the C-terminal carboxylic group of the inhibitors. This binding adopts a retro-manner principally stabilized by four possible hydrogen bonds. The Trp indole ring of the inhibitors is stacked against the imidazole of His143 in the S-1 site of the proteinase. Results from the study of synthetic inhibitor analogues showed the primary specificity of Trp residue of the inhibitors at the P-1 site, corroborating the stacking effect observed in our structures. Furthermore, we have made a detailed comparison of our structures with the binding modes of other inhibitors including batimastat, a hydroxamate inhibitor, and a barbiturate derivative. It suggests a close correlation between the inhibitory activity of an inhibitor and its ability to fill the S-1 pocket of the proteinase. Our work may provide insights into the rational design of small molecules that bind to this class of zinc-metalloproteinases.
-===Crystal Structure of a Taiwan Habu Venom Metalloproteinase complexed with pEKW.===
+Determinants of the inhibition of a Taiwan habu venom metalloproteinase by its endogenous inhibitors revealed by X-ray crystallography and synthetic inhibitor analogues.,Huang KF, Chiou SH, Ko TP, Wang AH Eur J Biochem. 2002 Jun;269(12):3047-56. PMID:12071970<ref>PMID:12071970</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_12071970}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1kuk" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12071970 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12071970}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-KUK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Protobothrops_mucrosquamatus Protobothrops mucrosquamatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KUK OCA].
-==Reference==
-Determinants of the inhibition of a Taiwan habu venom metalloproteinase by its endogenous inhibitors revealed by X-ray crystallography and synthetic inhibitor analogues., Huang KF, Chiou SH, Ko TP, Wang AH, Eur J Biochem. 2002 Jun;269(12):3047-56. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12071970 12071970]
-[[Category: Atrolysin E]]
 [[Category: Protobothrops mucrosquamatus]]
-[[Category: Single protein]]
+[[Category: Chiou SH]]
-[[Category: Chiou, S H.]]
+[[Category: Huang KF]]
-[[Category: Huang, K F.]]
+[[Category: Ko TP]]
-[[Category: Ko, T P.]]
+[[Category: Wang AHJ]]
-[[Category: Wang, A H.J.]]
-[[Category: Alpha/beta protein]]
-[[Category: Retro-binding manner]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 11:01:48 2008''