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| | <StructureSection load='5jvl' size='340' side='right'caption='[[5jvl]], [[Resolution|resolution]] 2.90Å' scene=''> | | <StructureSection load='5jvl' size='340' side='right'caption='[[5jvl]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5jvl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Clustered_yellowtops Clustered yellowtops]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JVL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JVL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5jvl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Flaveria_trinervia Flaveria trinervia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JVL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6NQ:2-BROMO-2-DEOXYADENOSINE+5-[BETA,GAMMA-IMIDE]TRIPHOSPHORIC+ACID'>6NQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</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]] 2.9Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PPDK, PDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4227 Clustered yellowtops])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6NQ:2-BROMO-2-DEOXYADENOSINE+5-[BETA,GAMMA-IMIDE]TRIPHOSPHORIC+ACID'>6NQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate,_phosphate_dikinase Pyruvate, phosphate dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.1 2.7.9.1] </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=5jvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jvl OCA], [https://pdbe.org/5jvl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jvl RCSB], [https://www.ebi.ac.uk/pdbsum/5jvl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jvl ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5jvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jvl OCA], [http://pdbe.org/5jvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jvl RCSB], [http://www.ebi.ac.uk/pdbsum/5jvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jvl ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PPDK_FLATR PPDK_FLATR]] Formation of phosphoenolpyruvate, which is the primary acceptor of CO(2) in C4 and some Crassulacean acid metabolism plants. | + | [https://www.uniprot.org/uniprot/PPDK_FLATR PPDK_FLATR] Formation of phosphoenolpyruvate, which is the primary acceptor of CO(2) in C4 and some Crassulacean acid metabolism plants. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Clustered yellowtops]] | + | [[Category: Flaveria trinervia]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyruvate, phosphate dikinase]]
| + | [[Category: Groth G]] |
| - | [[Category: Groth, G]] | + | [[Category: Hoeppner A]] |
| - | [[Category: Hoeppner, A]] | + | [[Category: Minges A]] |
| - | [[Category: Minges, A]] | + | |
| - | [[Category: Conformational transition]]
| + | |
| - | [[Category: Nucleotide binding]]
| + | |
| - | [[Category: Phosphotransferase]]
| + | |
| - | [[Category: Swiveling mechanism]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
PPDK_FLATR Formation of phosphoenolpyruvate, which is the primary acceptor of CO(2) in C4 and some Crassulacean acid metabolism plants.
Publication Abstract from PubMed
Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP- and Pi-dependent formation of phosphoenolpyruvate from pyruvate in C4 -plants, but the reverse reaction forming ATP in bacteria and protozoa. The multi-domain enzyme is considered an efficient molecular machine that performs one of the largest single domain movements in proteins. However, a comprehensive understanding of the proposed swiveling domain motion has been limited by not knowing structural intermediates or molecular dynamics of the catalytic process. Here, we present crystal structures of PPDKs from Flaveria, a model genus for studying the evolution of C4 -enzymes from phylogenetic ancestors. These structures resolve yet unknown conformational intermediates and provide the first detailed view on the large conformational transitions of the protein in the catalytic cycle. Independently performed unrestrained MD simulations and configurational free energy calculations also identified these intermediates. In all, our experimental and computational data reveal strict coupling of the CD swiveling motion to the conformational state of the NBD. Moreover, structural asymmetries and nucleotide binding states in the PPDK dimer support an alternate binding change mechanism for this intriguing bioenergetic enzyme.
Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase.,Minges A, Ciupka D, Winkler C, Hoppner A, Gohlke H, Groth G Sci Rep. 2017 Mar 30;7:45389. doi: 10.1038/srep45389. PMID:28358005[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Minges A, Ciupka D, Winkler C, Hoppner A, Gohlke H, Groth G. Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase. Sci Rep. 2017 Mar 30;7:45389. doi: 10.1038/srep45389. PMID:28358005 doi:http://dx.doi.org/10.1038/srep45389
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