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| | ==Pyruvate kinase (PYK) from Trypanosoma brucei in the presence of Magnesium, PEP and F26BP== | | ==Pyruvate kinase (PYK) from Trypanosoma brucei in the presence of Magnesium, PEP and F26BP== |
| - | <StructureSection load='4hyv' size='340' side='right' caption='[[4hyv]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='4hyv' size='340' side='right'caption='[[4hyv]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4hyv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trybb Trybb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HYV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4hyv]] 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=4HYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HYV FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4hyw|4hyw]], [[3srk|3srk]], [[3qv6|3qv6]], [[3qv7|3qv7]], [[3qv8|3qv8]], [[3pp7|3pp7]], [[3hqn|3hqn]], [[3hqo|3hqo]], [[3hqp|3hqp]], [[3hqq|3hqq]]</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=4hyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hyv OCA], [https://pdbe.org/4hyv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hyv RCSB], [https://www.ebi.ac.uk/pdbsum/4hyv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hyv ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PYK1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5702 TRYBB])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_kinase Pyruvate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.40 2.7.1.40] </span></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=4hyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hyv OCA], [http://pdbe.org/4hyv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hyv RCSB], [http://www.ebi.ac.uk/pdbsum/4hyv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4hyv ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/KPYK1_TRYBB KPYK1_TRYBB] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Pyruvate Kinase|Pyruvate Kinase]] | + | *[[Pyruvate kinase 3D structures|Pyruvate kinase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pyruvate kinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Trybb]] | + | [[Category: Trypanosoma brucei brucei]] |
| - | [[Category: Fothergill-Gilmore, L A]] | + | [[Category: Fothergill-Gilmore LA]] |
| - | [[Category: McNae, I W]] | + | [[Category: McNae IW]] |
| - | [[Category: Michels, P A.M]] | + | [[Category: Michels PAM]] |
| - | [[Category: Morgan, H P]] | + | [[Category: Morgan HP]] |
| - | [[Category: Walkinshaw, M D]] | + | [[Category: Walkinshaw MD]] |
| - | [[Category: Zhong, W]] | + | [[Category: Zhong W]] |
| - | [[Category: 6-diphosphate binding]]
| + | |
| - | [[Category: Allosteric regulation]]
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| - | [[Category: Cytosol]]
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| - | [[Category: Fructose-2]]
| + | |
| - | [[Category: Phosphoenolpyruvate binding]]
| + | |
| - | [[Category: Tetramer]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
4hyv is a 2 chain structure with sequence from Trypanosoma brucei brucei. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
KPYK1_TRYBB
Publication Abstract from PubMed
The active site of pyruvate kinase (PYK) is located between the AC core of the enzyme and a mobile lid corresponding to domain B. Many PYK structures have already been determined, but the first `effector-only' structure and the first with PEP (the true natural substrate) are now reported for the enzyme from Trypanosoma brucei. PEP soaked into crystals of the enzyme with bound allosteric activator fructose 2,6-bisphosphate (F26BP) and Mg(2+) triggers a substantial 23 degrees rotation of the B domain `in crystallo', resulting in a partially closed active site. The interplay of side chains with Mg(2+) and PEP may explain the mechanism of the domain movement. Furthermore, it is apparent that when F26BP is present but PEP is absent Mg(2+) occupies a position that is distinct from the two canonical Mg(2+)-binding sites at the active site. This third site is adjacent to the active site and involves the same amino-acid side chains as in canonical site 1 but in altered orientations. Site 3 acts to sequester Mg(2+) in a `priming' position such that the enzyme is maintained in its R-state conformation. In this way, Mg(2+) cooperates with F26BP to ensure that the enzyme is in a conformation that has a high affinity for the substrate.
`In crystallo' substrate binding triggers major domain movements and reveals magnesium as a co-activator of Trypanosoma brucei pyruvate kinase.,Zhong W, Morgan HP, McNae IW, Michels PA, Fothergill-Gilmore LA, Walkinshaw MD Acta Crystallogr D Biol Crystallogr. 2013 Sep 1;69(Pt 9):1768-79. doi:, 10.1107/S0907444913013875. Epub 2013 Aug 17. PMID:23999300[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Zhong W, Morgan HP, McNae IW, Michels PA, Fothergill-Gilmore LA, Walkinshaw MD. `In crystallo' substrate binding triggers major domain movements and reveals magnesium as a co-activator of Trypanosoma brucei pyruvate kinase. Acta Crystallogr D Biol Crystallogr. 2013 Sep 1;69(Pt 9):1768-79. doi:, 10.1107/S0907444913013875. Epub 2013 Aug 17. PMID:23999300 doi:10.1107/S0907444913013875
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