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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>
3PFL 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: 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''

Latest revision as of 13:40, 21 February 2024

CRYSTAL STRUCTURE OF PFL FROM E.COLI IN COMPLEX WITH SUBSTRATE ANALOGUE OXAMATECRYSTAL STRUCTURE OF PFL FROM E.COLI IN COMPLEX WITH SUBSTRATE ANALOGUE OXAMATE

Structural highlights

3pfl is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

3pfl, resolution 2.60Å

Drag the structure with the mouse to rotate

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