View source for 5jvn


==C3-type pyruvate phosphate dikinase: intermediate state of the central domain in the swiveling mechanism==
<StructureSection load='5jvn' size='340' side='right'caption='[[5jvn]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5jvn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Flaveria_pringlei Flaveria pringlei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JVN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JVN 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]] 2.9&#8491;</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5jvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jvn OCA], [https://pdbe.org/5jvn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jvn RCSB], [https://www.ebi.ac.uk/pdbsum/5jvn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jvn ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PPDK_FLAPR PPDK_FLAPR] Formation of phosphoenolpyruvate.
<div style="background-color:#fffaf0;">
== 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<ref>PMID:28358005</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5jvn" style="background-color:#fffaf0;"></div>

==See Also==
*[[Pyruvate phosphate dikinase|Pyruvate phosphate dikinase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Flaveria pringlei]]
[[Category: Large Structures]]
[[Category: Groth G]]
[[Category: Hoeppner A]]
[[Category: Minges A]]