2ez4: Difference between revisions

From Proteopedia
Jump to navigationJump to search
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
New page: left|200px<br /><applet load="2ez4" size="450" color="white" frame="true" align="right" spinBox="true" caption="2ez4, resolution 2.03Å" /> '''Pyruvate oxidase var...
 
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2ez4.gif|left|200px]]<br /><applet load="2ez4" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2ez4, resolution 2.03&Aring;" />
'''Pyruvate oxidase variant F479W'''<br />


==Overview==
==Pyruvate oxidase variant F479W==
Enzymes that use the cofactor thiamin diphosphate (ThDP, 1), the, biologically active form of vitamin B(1), are involved in numerous, metabolic pathways in all organisms. Although a theory of the cofactor's, underlying reaction mechanism has been established over the last five, decades, the three-dimensional structures of most major reaction, intermediates of ThDP enzymes have remained elusive. Here, we report the, X-ray structures of key intermediates in the oxidative decarboxylation of, pyruvate, a central reaction in carbon metabolism catalyzed by the ThDP-, and flavin-dependent enzyme pyruvate oxidase (POX)3 from Lactobacillus, plantarum. The structures of 2-lactyl-ThDP (LThDP, 2) and its stable, phosphonate analog, of 2-hydroxyethyl-ThDP (HEThDP, 3) enamine and of, 2-acetyl-ThDP (AcThDP, 4; all shown bound to the enzyme's active site), provide profound insights into the chemical mechanisms and the, stereochemical course of thiamin catalysis. These snapshots also suggest a, mechanism for a phosphate-linked acyl transfer coupled to electron, transfer in a radical reaction of pyruvate oxidase.
<StructureSection load='2ez4' size='340' side='right'caption='[[2ez4]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2ez4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactiplantibacillus_plantarum Lactiplantibacillus plantarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EZ4 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]] 2.03&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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=2ez4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ez4 OCA], [https://pdbe.org/2ez4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ez4 RCSB], [https://www.ebi.ac.uk/pdbsum/2ez4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ez4 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/POXB_LACPL POXB_LACPL] Important for the aerobic growth. Decarboxylates pyruvate in four steps. The energy released is partially stored in acetyl phosphate.
== 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/ez/2ez4_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=2ez4 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Enzymes that use the cofactor thiamin diphosphate (ThDP, 1), the biologically active form of vitamin B(1), are involved in numerous metabolic pathways in all organisms. Although a theory of the cofactor's underlying reaction mechanism has been established over the last five decades, the three-dimensional structures of most major reaction intermediates of ThDP enzymes have remained elusive. Here, we report the X-ray structures of key intermediates in the oxidative decarboxylation of pyruvate, a central reaction in carbon metabolism catalyzed by the ThDP- and flavin-dependent enzyme pyruvate oxidase (POX)3 from Lactobacillus plantarum. The structures of 2-lactyl-ThDP (LThDP, 2) and its stable phosphonate analog, of 2-hydroxyethyl-ThDP (HEThDP, 3) enamine and of 2-acetyl-ThDP (AcThDP, 4; all shown bound to the enzyme's active site) provide profound insights into the chemical mechanisms and the stereochemical course of thiamin catalysis. These snapshots also suggest a mechanism for a phosphate-linked acyl transfer coupled to electron transfer in a radical reaction of pyruvate oxidase.


==About this Structure==
The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography.,Wille G, Meyer D, Steinmetz A, Hinze E, Golbik R, Tittmann K Nat Chem Biol. 2006 Jun;2(6):324-8. Epub 2006 May 7. PMID:16680160<ref>PMID:16680160</ref>
2EZ4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_plantarum Lactobacillus plantarum] with MG, NA, PO4, TPP and FAD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Pyruvate_oxidase Pyruvate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.3.3 1.2.3.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2EZ4 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography., Wille G, Meyer D, Steinmetz A, Hinze E, Golbik R, Tittmann K, Nat Chem Biol. 2006 Jun;2(6):324-8. Epub 2006 May 7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16680160 16680160]
</div>
[[Category: Lactobacillus plantarum]]
<div class="pdbe-citations 2ez4" style="background-color:#fffaf0;"></div>
[[Category: Pyruvate oxidase]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Golbik, R.]]
__TOC__
[[Category: Hinze, E.]]
</StructureSection>
[[Category: Meyer, D.]]
[[Category: Lactiplantibacillus plantarum]]
[[Category: Steinmetz, A.]]
[[Category: Large Structures]]
[[Category: Tittmann, K.]]
[[Category: Golbik R]]
[[Category: Wille, G.]]
[[Category: Hinze E]]
[[Category: FAD]]
[[Category: Meyer D]]
[[Category: MG]]
[[Category: Steinmetz A]]
[[Category: NA]]
[[Category: Tittmann K]]
[[Category: PO4]]
[[Category: Wille G]]
[[Category: TPP]]
[[Category: tpp enzyme]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:14:32 2007''
Retrieved from "https://proteopedia.org/2ez4"