2c19: Difference between revisions

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-[[Image:2c19.gif|left|200px]]
- {{Structure
+==5-(4-Carboxy-2-oxo-butylsulfanyl)-4-oxo-pentanoic acid acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa==
-|PDB= 2c19 |SIZE=350|CAPTION= <scene name='initialview01'>2c19</scene>, resolution 2.05&Aring;
+<StructureSection load='2c19' size='340' side='right'caption='[[2c19]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Na+Binding+Site+For+Chain+A'>AC1</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=NA:SODIUM ION'>NA</scene>
+<table><tr><td colspan='2'>[[2c19]] 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=2C19 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C19 FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Porphobilinogen_synthase Porphobilinogen synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.24 4.2.1.24]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C1X:(Z)-N~6~-[(4R,5S)-5-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)DIHYDRO-2H-THIOPYRAN-3(4H)-YLIDENE]-L-LYSINE'>C1X</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=2c19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c19 OCA], [https://pdbe.org/2c19 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c19 RCSB], [https://www.ebi.ac.uk/pdbsum/2c19 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c19 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/c1/2c19_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=2c19 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-(4-CARBOXY-2-OXO-BUTYLSULFANYL)-4-OXO-PENTANOIC ACID 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 2c19" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-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.
+*[[Porphobilinogen synthase|Porphobilinogen synthase]]
+== References ==
-==About this Structure==
+<references/>
-C19 is a [[Single protein]] structure of sequence 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=2C19 OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-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:[http://www.ncbi.nlm.nih.gov/pubmed/16819823 16819823]
-[[Category: Porphobilinogen synthase]]
 [[Category: Pseudomonas aeruginosa]]
-[[Category: Single protein]]
+[[Category: Frankenberg-Dinkel N]]
-[[Category: Frankenberg-Dinkel, N.]]
+[[Category: Frere F]]
-[[Category: Frere, F.]]
+[[Category: Gacond S]]
-[[Category: Gacond, S.]]
+[[Category: Heinz DW]]
-[[Category: Heinz, D W.]]
+[[Category: Neier R]]
-[[Category: Neier, R.]]
+[[Category: Nentwich M]]
-[[Category: Nentwich, M.]]
-[[Category: MG]]
-[[Category: NA]]
-[[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 Thu Mar 20 16:09:27 2008''