1p3e: Difference between revisions

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-[[Image:1p3e.png|left|200px]]
-{{STRUCTURE_1p3e|  PDB=1p3e  |  SCENE=  }}
+==Structure of Glu endopeptidase in complex with MPD==
+<StructureSection load='1p3e' size='340' side='right'caption='[[1p3e]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1p3e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_intermedius Bacillus intermedius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P3E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P3E 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]] 1.72&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=1p3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p3e OCA], [https://pdbe.org/1p3e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p3e RCSB], [https://www.ebi.ac.uk/pdbsum/1p3e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p3e ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9EXR9_BACIN Q9EXR9_BACIN]
+== 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/p3/1p3e_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=1p3e ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Extracellular glutamyl endopeptidase from Bacillus intermedius (BIEP) is a chymotrypsin-like serine protease which cleaves the peptide bond on the carboxyl side of glutamic acid. Its three-dimensional structure was determined for C222(1) and C2 crystal forms of BIEP to 1.5 and 1.75 A resolution, respectively. The topology of BIEP diverges from the most common chymotrypsin architecture, because one of the domains consists of a beta-sandwich consisting of two antiparallel beta-sheets and two helices. In the C2 crystals, a 2-methyl-2,4-pentanediol (MPD) molecule was found in the substrate binding site, mimicking a glutamic acid. This enabled the identification of the residues involved in the substrate recognition. The presence of the MPD molecule causes a change in the active site; the interaction between two catalytic residues (His47 and Ser171) is disrupted. The N-terminal end of the enzyme is involved in the formation of the substrate binding pocket. This indicates a direct relation between zymogen activation and substrate charge compensation.
-===Structure of Glu endopeptidase in complex with MPD===
+The crystal structure of glutamyl endopeptidase from Bacillus intermedius reveals a structural link between zymogen activation and charge compensation.,Meijers R, Blagova EV, Levdikov VM, Rudenskaya GN, Chestukhina GG, Akimkina TV, Kostrov SV, Lamzin VS, Kuranova IP Biochemistry. 2004 Mar 16;43(10):2784-91. PMID:15005613<ref>PMID:15005613</ref>
-{{ABSTRACT_PUBMED_15005613}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1p3e" style="background-color:#fffaf0;"></div>
-[[1p3e]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_intermedius Bacillus intermedius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P3E OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:015005613</ref><references group="xtra"/>
+</StructureSection>
 [[Category: Bacillus intermedius]]
-[[Category: Akimkina, T V.]]
+[[Category: Large Structures]]
-[[Category: Blagova, E V.]]
+[[Category: Akimkina TV]]
-[[Category: Chestukhina, G G.]]
+[[Category: Blagova EV]]
-[[Category: Kostrov, S V.]]
+[[Category: Chestukhina GG]]
-[[Category: Kuranova, I P.]]
+[[Category: Kostrov SV]]
-[[Category: Lamzin, V S.]]
+[[Category: Kuranova IP]]
-[[Category: Levdikov, V M.]]
+[[Category: Lamzin VS]]
-[[Category: Meijers, R.]]
+[[Category: Levdikov VM]]
-[[Category: Rudenskaya, G N.]]
+[[Category: Meijers R]]
-[[Category: Glu specific]]
+[[Category: Rudenskaya GN]]
-[[Category: Hydrolase]]
-[[Category: Serine protease]]