2pfl: Difference between revisions
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==CRYSTAL STRUCTURE OF PFL FROM E.COLI== | ==CRYSTAL STRUCTURE OF PFL FROM E.COLI== | ||
<StructureSection load='2pfl' size='340' side='right' caption='[[2pfl]], [[Resolution|resolution]] 2.90Å' scene=''> | <StructureSection load='2pfl' size='340' side='right' caption='[[2pfl]], [[Resolution|resolution]] 2.90Å' scene=''> | ||
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pfl OCA], [http://pdbe.org/2pfl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pfl RCSB], [http://www.ebi.ac.uk/pdbsum/2pfl PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pfl OCA], [http://pdbe.org/2pfl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pfl RCSB], [http://www.ebi.ac.uk/pdbsum/2pfl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pfl ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pf/2pfl_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pf/2pfl_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
Revision as of 12:03, 29 August 2018
CRYSTAL STRUCTURE OF PFL FROM E.COLICRYSTAL STRUCTURE OF PFL FROM E.COLI
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedPyruvate 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. 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:10504733[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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