1x12: Difference between revisions

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-[[Image:1x12.png|left|200px]]
-<!--
+==Structure of Mutant Pyrrolidone Carboxyl Peptidase (E192D) from a Hyperthermophile, Pyrococcus furiosus==
-The line below this paragraph, containing "STRUCTURE_1x12", creates the "Structure Box" on the page.
+<StructureSection load='1x12' size='340' side='right'caption='[[1x12]], [[Resolution|resolution]] 2.00&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'>[[1x12]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X12 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]] 2&#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=1x12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x12 OCA], [https://pdbe.org/1x12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x12 RCSB], [https://www.ebi.ac.uk/pdbsum/1x12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x12 ProSAT]</span></td></tr>
-{{STRUCTURE_1x12|  PDB=1x12  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PCP_PYRFU PCP_PYRFU] Removes 5-oxoproline from various penultimate amino acid residues except L-proline.[HAMAP-Rule:MF_00417]
+== 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/x1/1x12_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=1x12 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Pyrrolidone carboxyl peptidases (PCPs) from hyperthermophiles have a structurally conserved and completely buried Glu192 in the hydrophobic core; in contrast, the corresponding residue in the mesophile protein is a hydrophobic residue, Ile. Does the buried ionizable residue contribute to stabilization or destabilization of hyperthermophile PCPs? To elucidate the role of the buried glutamic acid in stabilizing PCP from hyperthermophiles, we constructed five Glu192 mutants of PCP-0SH (C142S/C188S, Cys-free double mutant of PCP) from Pyrococcus furiosus and examined their thermal and pH-induced unfolding and crystal structures and compared them with those of PCP-0SH. The stabilities of apolar (E192A/I/V) and polar (E192D/Q) mutants were less than PCP-0SH at acidic pH values. In the alkaline region, the mutant proteins, except for E192D, were more stable than PCP-0SH. The thermal stability data and theoretical calculations indicated an apparent pKa value &gt; or = 7.3 for Glu192. Present results confirmed that the protonated Glu192 in PCP-0SH forms strong hydrogen bonds with the carbonyl oxygen and peptide nitrogen of Pro168. New intermolecular hydrogen bonds in the E --&gt; A/D mutants were formed by a water molecule introduced into the cavity created around position 192, whereas the hydrogen bonds disappeared in the E --&gt; I/V mutants. Structure-based empirical stability of mutant proteins was in good agreement with the experimental results. The results indicated that (1) completely buried Glu192 contributes to the stabilization of PCP-0SH because of the formation of strong intramolecular hydrogen bonds and (2) the hydrogen bonds by the nonionized and buried Glu can contribute more than the burial of hydrophobic groups to the conformational stability of proteins.
-===Structure of Mutant Pyrrolidone Carboxyl Peptidase (E192D) from a Hyperthermophile, Pyrococcus furiosus===
+Completely buried, non-ion-paired glutamic acid contributes favorably to the conformational stability of pyrrolidone carboxyl peptidases from hyperthermophiles.,Kaushik JK, Iimura S, Ogasahara K, Yamagata Y, Segawa S, Yutani K Biochemistry. 2006 Jun 13;45(23):7100-12. PMID:16752900<ref>PMID:16752900</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_16752900}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1x12" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16752900 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16752900}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[1x12]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X12 OCA].
-==Reference==
-<ref group="xtra">PMID:16752900</ref><ref group="xtra">PMID:11432786</ref><references group="xtra"/>
 [[Category: Pyrococcus furiosus]]
-[[Category: Pyroglutamyl-peptidase I]]
+[[Category: Kaushik JK]]
-[[Category: Kaushik, J K.]]
+[[Category: Ogasahara K]]
-[[Category: Ogasahara, K.]]
+[[Category: Yamagata Y]]
-[[Category: Yamagata, Y.]]
+[[Category: Yutani K]]
-[[Category: Yutani, K.]]
-[[Category: Hydrolase]]
-[[Category: Stability of protein]]