1qdm: Difference between revisions

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-[[Image:1qdm.gif|left|200px]]<br /><applet load="1qdm" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1qdm, resolution 2.3&Aring;" />
-'''CRYSTAL STRUCTURE OF PROPHYTEPSIN, A ZYMOGEN OF A BARLEY VACUOLAR ASPARTIC PROTEINASE.'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF PROPHYTEPSIN, A ZYMOGEN OF A BARLEY VACUOLAR ASPARTIC PROTEINASE.==
-We determined at 2.3 A resolution the crystal structure of prophytepsin, a, zymogen of a barley vacuolar aspartic proteinase. In addition to the, classical pepsin-like bilobal main body of phytepsin, we also traced most, of the propeptide, as well as an independent plant-specific domain, never, before described in structural terms. The structure revealed that, in, addition to the propeptide, 13 N-terminal residues of the mature phytepsin, are essential for inactivation of the enzyme. Comparison of the, plant-specific domain with NK-lysin indicates that these two saposin-like, structures are closely related, suggesting that all saposins and, saposin-like domains share a common topology. Structural analysis of, prophytepsin led to the identification of a putative membrane, receptor-binding site involved in Golgi-mediated transport to vacuoles.
+<StructureSection load='1qdm' size='340' side='right'caption='[[1qdm]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1qdm]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QDM 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]] 2.3&#8491;</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=1qdm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qdm OCA], [https://pdbe.org/1qdm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qdm RCSB], [https://www.ebi.ac.uk/pdbsum/1qdm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qdm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ASPR_HORVU ASPR_HORVU] Involved in the breakdown of propeptides of storage proteins in protein-storage vacuoles (By similarity).
+== 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/qd/1qdm_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=1qdm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We determined at 2.3 A resolution the crystal structure of prophytepsin, a zymogen of a barley vacuolar aspartic proteinase. In addition to the classical pepsin-like bilobal main body of phytepsin, we also traced most of the propeptide, as well as an independent plant-specific domain, never before described in structural terms. The structure revealed that, in addition to the propeptide, 13 N-terminal residues of the mature phytepsin are essential for inactivation of the enzyme. Comparison of the plant-specific domain with NK-lysin indicates that these two saposin-like structures are closely related, suggesting that all saposins and saposin-like domains share a common topology. Structural analysis of prophytepsin led to the identification of a putative membrane receptor-binding site involved in Golgi-mediated transport to vacuoles.
-==About this Structure==
+Crystal structure of plant aspartic proteinase prophytepsin: inactivation and vacuolar targeting.,Kervinen J, Tobin GJ, Costa J, Waugh DS, Wlodawer A, Zdanov A EMBO J. 1999 Jul 15;18(14):3947-55. PMID:10406799<ref>PMID:10406799</ref>
-QDM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Active as [http://en.wikipedia.org/wiki/Phytepsin Phytepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.40 3.4.23.40] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QDM OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structure of plant aspartic proteinase prophytepsin: inactivation and vacuolar targeting., Kervinen J, Tobin GJ, Costa J, Waugh DS, Wlodawer A, Zdanov A, EMBO J. 1999 Jul 15;18(14):3947-55. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10406799 10406799]
+</div>
+<div class="pdbe-citations 1qdm" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Hordeum vulgare]]
-[[Category: Phytepsin]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Costa J]]
-[[Category: Costa, J.]]
+[[Category: Kervinen J]]
-[[Category: Kervinen, J.]]
+[[Category: Tobin GJ]]
-[[Category: Tobin, G.J.]]
+[[Category: Waugh DS]]
-[[Category: Waugh, D.S.]]
+[[Category: Wlodawer A]]
-[[Category: Wlodawer, A.]]
+[[Category: Zdanov A]]
-[[Category: Zdanov, A.]]
-[[Category: aspartic proteinases]]
-[[Category: phytepsin]]
-[[Category: saposin-like domain]]
-[[Category: zymogen structure]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:36:02 2007''