5JVN
C3-type pyruvate phosphate dikinase: intermediate state of the central domain in the swiveling mechanism
Summary for 5JVN
| Entry DOI | 10.2210/pdb5jvn/pdb |
| Descriptor | Pyruvate, phosphate dikinase, chloroplastic, 2'-Bromo-2'-deoxyadenosine 5'-[beta,gamma-imide]triphosphoric acid, PHOSPHOENOLPYRUVATE, ... (4 entities in total) |
| Functional Keywords | phosphotransferase, nucleotide binding, conformational transition, swiveling mechanism, transferase |
| Biological source | Flaveria pringlei |
| Total number of polymer chains | 1 |
| Total formula weight | 96329.87 |
| Authors | Minges, A.,Hoeppner, A.,Groth, G. (deposition date: 2016-05-11, release date: 2017-04-05, Last modification date: 2024-01-10) |
| Primary citation | 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, 7:45389-45389, 2017 Cited by PubMed Abstract: Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP- and P-dependent formation of phosphoenolpyruvate from pyruvate in C -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 C -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. PubMed: 28358005DOI: 10.1038/srep45389 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.9 Å) |
Structure validation
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