3pfl: Difference between revisions

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-[[Image:3pfl.jpg|left|200px]]<br /><applet load="3pfl" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="3pfl, resolution 2.60&Aring;" />
-'''CRYSTAL STRUCTURE OF PFL FROM E.COLI IN COMPLEX WITH SUBSTRATE ANALOGUE OXAMATE'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF PFL FROM E.COLI IN COMPLEX WITH SUBSTRATE ANALOGUE OXAMATE==
-Pyruvate formate-lyase (PFL) from Escherichia coli uses a radical mechanism to reversibly cleave the C1-C2 bond of pyruvate using the Gly 734 radical and two cysteine residues (Cys 418, Cys 419). We have determined by X-ray crystallography the structures of PFL (non-radical form), its complex with the substrate analog oxamate, and the C418A,C419A double mutant. The atomic model (a dimer of 759-residue monomers) comprises a 10-stranded beta/alpha barrel assembled in an antiparallel manner from two parallel five-stranded beta-sheets; this architecture resembles that of ribonucleotide reductases. Gly 734 and Cys 419, positioned at the tips of opposing hairpin loops, meet in the apolar barrel center (Calpha-Sgamma = 3.7 A). Oxamate fits into a compact pocket where C2 is juxtaposed with Cys 418Sgamma (3.3 A), which in turn is close to Cys 419Sgamma (3.7 A). Our model of the active site is suggestive of a snapshot of the catalytic cycle, when the pyruvate-carbonyl awaits attack by the Cys 418 thiyl radical. We propose a homolytic radical mechanism for PFL that involves Cys 418 and Cys 419 both as thiyl radicals, with distinct chemical functions.
+<StructureSection load='3pfl' size='340' side='right'caption='[[3pfl]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[3pfl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PFL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PFL FirstGlance]. <br>
-PFL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=OXM:'>OXM</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Formate_C-acetyltransferase Formate C-acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.54 2.3.1.54] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PFL OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OXM:OXAMIC+ACID'>OXM</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pfl OCA], [https://pdbe.org/3pfl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pfl RCSB], [https://www.ebi.ac.uk/pdbsum/3pfl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pfl ProSAT]</span></td></tr>
-Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase., Becker A, Fritz-Wolf K, Kabsch W, Knappe J, Schultz S, Volker Wagner AF, Nat Struct Biol. 1999 Oct;6(10):969-75. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10504733 10504733]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PFLB_ECOLI PFLB_ECOLI]
+== 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/pf/3pfl_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=3pfl ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Formate C-acetyltransferase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Becker A]]
-[[Category: Becker, A.]]
+[[Category: Fritz-Wolf K]]
-[[Category: Fritz-Wolf, K.]]
+[[Category: Kabsch W]]
-[[Category: Kabsch, W.]]
+[[Category: Knappe J]]
-[[Category: Knappe, J.]]
+[[Category: Schultz S]]
-[[Category: Schultz, S.]]
+[[Category: Wagner AFV]]
-[[Category: Wagner, A F.V.]]
-[[Category: OXM]]
-[[Category: glucose metabolism]]
-[[Category: glycyl radical enzyme]]
-[[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:10:50 2008''