3c8f: Difference between revisions

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[[Image:3c8f.png|left|200px]]


{{STRUCTURE_3c8f| PDB=3c8f | SCENE= }}
==4Fe-4S-Pyruvate formate-lyase Activating Enzyme with partially disordered AdoMet==
<StructureSection load='3c8f' size='340' side='right'caption='[[3c8f]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3c8f]] is a 1 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=3C8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C8F FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MT2:[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)METHYLSULFONIUM'>MT2</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [https://pdbe.org/3c8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [https://www.ebi.ac.uk/pdbsum/3c8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c8f ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PFLA_ECOLI PFLA_ECOLI] Activation of pyruvate formate-lyase 1 under anaerobic conditions by generation of an organic free radical, using S-adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine.
== 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/c8/3c8f_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=3c8f ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Pyruvate formate-lyase activating enzyme generates a stable and catalytically essential glycyl radical on G(734) of pyruvate formate-lyase via the direct, stereospecific abstraction of a hydrogen atom from pyruvate formate-lyase. The activase performs this remarkable feat by using an iron-sulfur cluster and S-adenosylmethionine (AdoMet), thus placing it among the AdoMet radical superfamily of enzymes. We report here structures of the substrate-free and substrate-bound forms of pyruvate formate-lyase-activating enzyme, the first structures of an AdoMet radical activase. To obtain the substrate-bound structure, we have used a peptide substrate, the 7-mer RVSGYAV, which contains the sequence surrounding G(734). Our structures provide fundamental insights into the interactions between the activase and the G(734) loop of pyruvate formate-lyase and provide a structural basis for direct and stereospecific H atom abstraction from the buried G(734) of pyruvate formate-lyase.


===4Fe-4S-Pyruvate formate-lyase Activating Enzyme with partially disordered AdoMet===
Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme.,Vey JL, Yang J, Li M, Broderick WE, Broderick JB, Drennan CL Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16137-41. Epub 2008 Oct 13. PMID:18852451<ref>PMID:18852451</ref>


{{ABSTRACT_PUBMED_18852451}}
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
==About this Structure==
<div class="pdbe-citations 3c8f" style="background-color:#fffaf0;"></div>
[[3c8f]] is a 1 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=3C8F OCA].
== References ==
 
<references/>
==Reference==
__TOC__
<ref group="xtra">PMID:018852451</ref><references group="xtra"/>
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Drennan, C L.]]
[[Category: Large Structures]]
[[Category: Vey, J L.]]
[[Category: Drennan CL]]
[[Category: Activase]]
[[Category: Vey JL]]
[[Category: Adomet radical]]
[[Category: Carbohydrate metabolism]]
[[Category: Glucose metabolism]]
[[Category: Glycyl radical]]
[[Category: Iron]]
[[Category: Iron-sulfur]]
[[Category: Metal-binding]]
[[Category: Oxidoreductase]]
[[Category: S-adenosyl-l-methionine]]
[[Category: Sam radical]]

Latest revision as of 09:00, 13 August 2026

4Fe-4S-Pyruvate formate-lyase Activating Enzyme with partially disordered AdoMet

3c8f, resolution 2.25Å

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