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1kuf

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(New page: 200px<br /><applet load="1kuf" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kuf, resolution 1.35&Aring;" /> '''High-resolution Crys...)
Current revision (08:03, 3 April 2024) (edit) (undo)
 
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[[Image:1kuf.gif|left|200px]]<br /><applet load="1kuf" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1kuf, resolution 1.35&Aring;" />
 
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'''High-resolution Crystal Structure of a Snake Venom Metalloproteinase from Taiwan Habu'''<br />
 
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==Overview==
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==High-resolution Crystal Structure of a Snake Venom Metalloproteinase from Taiwan Habu==
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The crystal structure of TM-3, a small snake-venom metalloproteinase, (SVMP) isolated from Taiwan habu (Trimeresurus mucrosquamatus), was, determined at 1.35 A resolution with resultant R and R(free) values of, 0.181 and 0.204, respectively. The overall structure of TM-3 is an oblate, ellipsoid that contains three disulfide crosslinks, Cys118-Cys197, Cys159-Cys181 and Cys161-Cys164. It exhibits the typical structural, features of SVMPs and is closely related to the structure of the catalytic, proteinase domain of TNFalpha-converting enzyme (TACE). In the present, structure, the essential catalytic zinc ion was found to be replaced by a, cadmium ion during crystallization, as revealed by atomic absorption, analysis and X-ray data. This cadmium ion is bound to six ligands, including three conserved histidines and three water molecules, displaying, the coordination geometry of a distorted octahedron. One of the water, molecules is proposed to play the role of stabilizing the tetrahedral, intermediate during the catalysis of SVMPs. The putative S'(1) specificity, pocket of TM-3 is relatively shallow, in contrast to the deep pockets of, adamalysin II, atrolysin C and H(2)-proteinase, but is similar to those in, acutolysin A and TACE. The shallow pocket is a consequence of the presence, of the non-conserved disulfide bond Cys159-Cys181 and the residue Gln174, at the bottom of the S'(1) pocket. The results indicate that the, active-site structure of TM-3, among the know structures of SVMPs examined, thus far, is most similar to that of TACE owing to their close disulfide, configurations and the S'(1) specificity pocket.
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<StructureSection load='1kuf' size='340' side='right'caption='[[1kuf]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1kuf]] is a 1 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=1KUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KUF FirstGlance]. <br>
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1KUF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Protobothrops_mucrosquamatus Protobothrops mucrosquamatus] with CD as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Atrolysin_E Atrolysin E], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.44 3.4.24.44] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KUF OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.35&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kuf OCA], [https://pdbe.org/1kuf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kuf RCSB], [https://www.ebi.ac.uk/pdbsum/1kuf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kuf ProSAT]</span></td></tr>
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The 1.35 A structure of cadmium-substituted TM-3, a snake-venom metalloproteinase from Taiwan habu: elucidation of a TNFalpha-converting enzyme-like active-site structure with a distorted octahedral geometry of cadmium., Huang KF, Chiou SH, Ko TP, Yuann JM, Wang AH, Acta Crystallogr D Biol Crystallogr. 2002 Jul;58(Pt 7):1118-28. Epub 2002, Jun 20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12077431 12077431]
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</table>
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[[Category: Atrolysin E]]
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ku/1kuf_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1kuf ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Protobothrops mucrosquamatus]]
[[Category: Protobothrops mucrosquamatus]]
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[[Category: Single protein]]
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[[Category: Chiou SH]]
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[[Category: Chiou, S.H.]]
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[[Category: Huang KF]]
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[[Category: Huang, K.F.]]
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[[Category: Ko TP]]
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[[Category: Ko, T.P.]]
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[[Category: Wang AHJ]]
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[[Category: Wang, A.H.J.]]
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[[Category: Yuann JM]]
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[[Category: Yuann, J.M.]]
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[[Category: CD]]
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[[Category: alpha/beta protein]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 01:58:04 2007''
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Current revision

High-resolution Crystal Structure of a Snake Venom Metalloproteinase from Taiwan Habu

PDB ID 1kuf

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