5jvn | pdb_00005jvn

C3-type pyruvate phosphate dikinase: intermediate state of the central domain in the swiveling mechanism

spinqualitylabelsall models 5jvn, resolution 2.90Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5jvn is a 1 chain structure with sequence from Flaveria pringlei. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.9Å Ligands: 6NQ, MG, PEP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function PPDK_FLAPR Formation of phosphoenolpyruvate. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Pyruvate phosphate dikinase

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