2c13: Difference between revisions

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-{{Seed}}
-[[Image:2c13.png|left|200px]]
-<!--
+==5-hydroxy-levulinic acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa==
-The line below this paragraph, containing "STRUCTURE_2c13", creates the "Structure Box" on the page.
+<StructureSection load='2c13' size='340' side='right'caption='[[2c13]], [[Resolution|resolution]] 2.15&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'>[[2c13]] 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=2C13 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C13 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]] 2.15&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FHL:(E)-N~6~-[3-CARBOXY-1-(HYDROXYMETHYL)PROPYLIDENE]-L-LYSINE'>FHL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-{{STRUCTURE_2c13|  PDB=2c13  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2c13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c13 OCA], [https://pdbe.org/2c13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c13 RCSB], [https://www.ebi.ac.uk/pdbsum/2c13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c13 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HEM2_PSEAE HEM2_PSEAE] Catalyzes an early step in the biosynthesis of tetrapyrroles. Binds two molecules of 5-aminolevulinate per subunit, each at a distinct site, and catalyzes their condensation to form porphobilinogen (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/c1/2c13_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=2c13 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Porphobilinogen synthase catalyzes the first committed step of the tetrapyrrole biosynthesis pathway. In an aldol-like condensation, two molecules of 5-aminolevulinic acid (ALA) form the first pyrrole, porphobilinogen. Newly synthesized analogues of a reaction intermediate of porphobilinogen synthase have been employed in studying the active site and the catalytic mechanism of this early enzyme of tetrapyrrole biosynthesis. This study combines structural and kinetic evaluation of the inhibition potency of these inhibitors. In addition, one of the determined protein structures provides for the first time structural evidence of a magnesium ion in the active site. From these results, we can corroborate an earlier postulated enzymatic mechanism that starts with formation of a C-C bond, linking C3 of the A-side ALA to C4 of the P-side ALA through an aldole addition. The obtained data are discussed with respect to the current literature.
-===5-HYDROXY-LEVULINIC ACID BOUND TO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA===
+Probing the active site of Pseudomonas aeruginosa porphobilinogen synthase using newly developed inhibitors.,Frere F, Nentwich M, Gacond S, Heinz DW, Neier R, Frankenberg-Dinkel N Biochemistry. 2006 Jul 11;45(27):8243-53. PMID:16819823<ref>PMID:16819823</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2c13" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16819823}}, adds the Publication Abstract to the page
+*[[Porphobilinogen synthase|Porphobilinogen synthase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16819823 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16819823}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-C13 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=2C13 OCA].
-==Reference==
-<ref group="xtra">PMID:16819823</ref><references group="xtra"/>
-[[Category: Porphobilinogen synthase]]
 [[Category: Pseudomonas aeruginosa]]
-[[Category: Frankenberg-Dinkel, N.]]
+[[Category: Frankenberg-Dinkel N]]
-[[Category: Frere, F.]]
+[[Category: Frere F]]
-[[Category: Gacond, S.]]
+[[Category: Gacond S]]
-[[Category: Heinz, D W.]]
+[[Category: Heinz DW]]
-[[Category: Neier, R.]]
+[[Category: Neier R]]
-[[Category: Nentwich, M.]]
+[[Category: Nentwich M]]
-[[Category: Cocrystallization]]
-[[Category: Enzyme mechanism]]
-[[Category: Lyase]]
-[[Category: Metalloenzyme]]
-[[Category: Porphobilinogen synthase]]
-[[Category: Porphyrin biosynthesis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:21:53 2009''