2zxc: Difference between revisions

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-{{Seed}}
-[[Image:2zxc.png|left|200px]]
-<!--
+==Ceramidase complexed with C2==
-The line below this paragraph, containing "STRUCTURE_2zxc", creates the "Structure Box" on the page.
+<StructureSection load='2zxc' size='340' side='right'caption='[[2zxc]], [[Resolution|resolution]] 2.20&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'>[[2zxc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZXC 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]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2ED:N-[(1R,2R,3E)-2-HYDROXY-1-(HYDROXYMETHYL)HEPTADEC-3-EN-1-YL]ACETAMIDE'>2ED</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2zxc|  PDB=2zxc  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxc OCA], [https://pdbe.org/2zxc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zxc RCSB], [https://www.ebi.ac.uk/pdbsum/2zxc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zxc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NCASE_PSEAE NCASE_PSEAE] Catalyzes the cleavage of the N-acyl linkage of the ceramides (Cers) to yield sphingosine (Sph) and free fatty acid at an optimal pH of 8-9. Also catalyzes the synthesis of Cers from Sph and fatty acid.<ref>PMID:9603946</ref> <ref>PMID:19088069</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/zx/2zxc_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=2zxc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ceramidase (CDase; EC 3.5.1.23) hydrolyzes ceramide to generate sphingosine and fatty acid. The enzyme plays a regulatory role in a variety of physiological events in eukaryotes and also functions as an exotoxin in particular bacteria. The crystal structures of neutral CDase from Pseudomonas aeruginosa (PaCD) in the C2-ceramide-bound and -unbound forms were determined at 2.2 and 1.4 A resolutions, respectively. PaCD consists of two domains, and the Zn(2+)- and Mg(2+)/Ca(2+)-binding sites are found within the center of the N-terminal domain and the interface between the domains, respectively. The structural comparison between the C2-ceramide-bound and unbound forms revealed an open-closed conformational change occurring to loop I upon binding of C2-ceramide. In the closed state, this loop sits above the Zn(2+) coordination site and over the opening to the substrate binding site. Mutational analyses of residues surrounding the Zn(2+) of PaCD and rat neutral CDase revealed that the cleavage or creation of the N-acyl linkage of ceramide follows a similar mechanism as observed for the Zn(2+)-dependent carboxypeptidases. The results provide an understanding of the molecular mechanism of hydrolysis and synthesis of ceramide by the enzyme. Furthermore, insights into the actions of PaCD and eukaryotic neutral CDases as an exotoxin and mediators of sphingolipid signaling are also revealed, respectively.
-===seramidase complexed with C2===
+Mechanistic insights into the hydrolysis and synthesis of ceramide by neutral ceramidase.,Inoue T, Okino N, Kakuta Y, Hijikata A, Okano H, Goda HM, Tani M, Sueyoshi N, Kambayashi K, Matsumura H, Kai Y, Ito M J Biol Chem. 2009 Apr 3;284(14):9566-77. Epub 2008 Dec 16. PMID:19088069<ref>PMID:19088069</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2zxc" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19088069}}, adds the Publication Abstract to the page
+*[[Ceramidase|Ceramidase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19088069 is the PubMed ID number.
+*[[Ceramidase 3D PDB structures|Ceramidase 3D PDB structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_19088069}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-ZXC is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZXC OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:19088069</ref><references group="xtra"/>
-[[Category: Ceramidase]]
 [[Category: Pseudomonas aeruginosa]]
-[[Category: Inoue, T.]]
+[[Category: Inoue T]]
-[[Category: Ito, M.]]
+[[Category: Ito M]]
-[[Category: Kakuta, Y.]]
+[[Category: Kakuta Y]]
-[[Category: Matsumura, H.]]
+[[Category: Matsumura H]]
-[[Category: Okano, H.]]
+[[Category: Okano H]]
-[[Category: Okino, N.]]
+[[Category: Okino N]]
-[[Category: Beta-prism fold surrounded by six alpha helix]]
-[[Category: Hydrolase]]
-[[Category: Lipid metabolism]]
-[[Category: Secreted]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 11 20:07:41 2009''