Pyruvate phosphate dikinase

You may also download the full High Resolution video.

Pyruvate phosphate dikinase (PPDK) catalyzes the inter-conversion of adenosine triphosphate (ATP), PO4-3, and pyruvate with adenine monophosphate (AMP), pyrophosphate (P2O7-4), and phosphoenolpyruvate (PEP) in the presence of Mg2+ and K+/Na+. The three-step reversible reaction proceeds via phosphoenzyme and pyrophosphoenzyme intermediates with a histidine residue serving as the phosphocarrier:

(1) PPDK-His + PEP ⇄ PPDK-His~PO3 + pyruvate

(2) PPDK-His~PO3 + P2O7 ⇄ PPDK-His~P2O7 + PO3

(3) PPDK-His~P2O7 + AMP ⇄ PPDK-His + ATP

The enzyme contains two remotely located reaction centers(~45 Å apart; the PEP/pyruvate partial reaction (step 1) takes place at the C-terminal domain (adopting an α/β barrel fold) and the nucleotide and inorganic phosphate partial reactions (steps 2 and 3) take place at the N-terminal domain (adopting the ATP grasp fold with two sub domains). A central domain, tethered to the N- and C-terminal domains by two closely-associated linkers, contains a phosphorylatable histidine residue (His455). To shuttle the phosphoryl group between the two reaction centers, the His-domain undergoes a ~110° swivel motion around the two linkers. In addition, upon detachment from the His-domain, the two nucleotide-binding sub domains undergo a ~40° hinge motion that opens the active site cleft.

The movie depicts the catalytic reaction involving three in-line phosphotransfers and the accompanied protein conformational transitions. This is a model based on crystal structures of PPDK in the two extreme conformational states and of complexes bound to substrate analogs, phosphonopyruvate and 5'-adenylyl-β,γ -imidodiphosphate (AMPPNP). The nucleotide binding subdomains are colored green and blue. The PEP binding domain is colored cyan. The His-domain is colored yellow, and the linker segments that connect the His-domain to the partner domains are colored red. Ligands and the catalytic histidine are depicted in stick models with the atomic color scheme: Carbon – gray, Nitrogen – blue, Oxygen – red, Phosphorous – green, Magnesium – magenta.

References:

1. Herzberg, O., Chen, C. C. H., Kapadia, G., McGuire, M., Carroll, L. J., Noh, S. J., Dunaway-Mariano, D. (1996) Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites, Proc Natl Acad Sci 93, 2652-2657.

2. Herzberg, O., Chen, C. C. H., Liu, S., Tempczyk, A., Howard, A., Wei, M., Ye, D., Dunaway-Mariano, D. (2002) Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis, Biochemistry 41, 780-787.

3. Lim, K., Read, R. J., Chen, C. C., Tempczyk, A., Wei, M., Ye, D., Wu, C., Dunaway-Mariano, D., and Herzberg, O. (2007) Swiveling domain mechanism in pyruvate phosphate dikinase, Biochemistry 46, 14845-14853.