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| | <StructureSection load='1cm5' size='340' side='right'caption='[[1cm5]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='1cm5' size='340' side='right'caption='[[1cm5]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1cm5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CM5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CM5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1cm5]] 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=1CM5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CM5 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1cm5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cm5 OCA], [http://pdbe.org/1cm5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cm5 RCSB], [http://www.ebi.ac.uk/pdbsum/1cm5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1cm5 ProSAT]</span></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=1cm5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cm5 OCA], [https://pdbe.org/1cm5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cm5 RCSB], [https://www.ebi.ac.uk/pdbsum/1cm5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cm5 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/PFLB_ECOLI PFLB_ECOLI] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| - | [[Category: Formate C-acetyltransferase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[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, A F.V]] | + | [[Category: Wagner AFV]] |
| - | [[Category: Glucose metabolism]]
| + | |
| - | [[Category: Glycyl radical enzyme]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
PFLB_ECOLI
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 PubMed
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.
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
- ↑ Becker A, Fritz-Wolf K, Kabsch W, Knappe J, Schultz S, Volker Wagner AF. Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase. Nat Struct Biol. 1999 Oct;6(10):969-75. PMID:10504733 doi:10.1038/13341
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