4kcv
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4kcv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KCV FirstGlance]. <br> | <table><tr><td colspan='2'>[[4kcv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KCV FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FDP:FRUCTOSE-2,6-DIPHOSPHATE'>FDP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.18Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FDP:FRUCTOSE-2,6-DIPHOSPHATE'>FDP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4kcv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcv OCA], [https://pdbe.org/4kcv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kcv RCSB], [https://www.ebi.ac.uk/pdbsum/4kcv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kcv 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=4kcv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcv OCA], [https://pdbe.org/4kcv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kcv RCSB], [https://www.ebi.ac.uk/pdbsum/4kcv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kcv ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/KPYK1_TRYBB KPYK1_TRYBB] | [https://www.uniprot.org/uniprot/KPYK1_TRYBB KPYK1_TRYBB] | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | The phosphotransfer mechanism of pyruvate kinases (PYKs) has been studied in detail, but the mechanism of the intrinsic decarboxylase reaction catalysed by PYKs is still unknown. 1H NMR was used in this work to follow oxaloacetate (OAA) decarboxylation by trypanosomatid and human PYKs confirming that the decarboxylase activity is conserved across distantly related species. Crystal structures of Trypanosoma brucei PYK (TbPYK) complexed with the product of the decarboxylase reaction (pyruvate), and a series of substrate analogues (D-malate, alpha-ketoglutarate and oxalate) show that the OAA analogues bind to the kinase active site with similar binding modes, confirming that both decarboxylase and kinase activities share a common site for substrate binding and catalysis. Decarboxylation of OAA as monitored by NMR for TbPYK is relatively slow with turn-over values of 0.86 s-1 and 1.47 s-1 in the absence and presence of fructose 2,6-bisphosphate (F26BP), respectively. Human M1PYK has a measured turn-over value of 0.50 s-1. The X-ray structures explain why the decarboxylation activity is specific for OAA and is not general for alpha-keto acid analogues. Conservation of the decarboxylase reaction across divergent species is a consequence of piggybacking on the conserved kinase mechanism which requires a stabilised enol intermediate. | ||
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| - | Pyruvate kinases have an intrinsic and conserved decarboxylase activity.,Zhong W, Morgan HP, Nowicki MW, McNae IW, Yuan M, Bella J, Michels PA, Fothergill-Gilmore LA, Walkinshaw MD Biochem J. 2013 Dec 13. PMID:24328825<ref>PMID:24328825</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 4kcv" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Pyruvate kinase 3D structures|Pyruvate kinase 3D structures]] | *[[Pyruvate kinase 3D structures|Pyruvate kinase 3D structures]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
Pyruvate kinase (PYK) from Trypanosoma brucei soaked with 2-oxoglutaric acid
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