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Pyruvate phosphate dikinase

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Pyruvate Phosphate Dikinase - a Molecular Machine

Pyruvate phosphate dikinase complex with sulfate ion 1dik.
Ligands:
Gene: PPDK (Clostridium symbiosum)
Activity: Pyruvate, phosphate dikinase, with EC number 2.7.9.1
Related: 2r82
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



<swf width="390" height="390">http://carb.umbi.umd.edu//system/files/users/herzberg/ppdk_release.swf</swf>

You may also download the full High Resolution video.

Pyruvate phosphate dikinase (PPDK) is an enzyme that catalyzes the inter-conversion of adenosine triphosphate (ATP), phosphate (Pi), and pyruvate with adenine monophosphate (AMP), pyrophosphate (PPi), and phosphoenolpyruvate (PEP) in the presence of magnesium and potassium/sodium ions (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 has been found in bacteria, in C4 and Crassulacean acid metabolism plants, and in parasites, but not in higher animal forms. In bacteria and parasites, PPDK functions in the direction of ATP synthesis (reminiscent of pyruvate kinase). In plants and in photosynthetic bacteria, PPDK functions in PEP formation, potentiating the rate of CO2 fixation that takes place during photosynthesis. PPDK exhibits sequence homology to pyruvate phosphate synthase, and to another enzyme that utilizes phosphotransfer from PEP to a histidine residues, Enzyme I of the PEP:sugar phosphotransferase system (PTS).

PPDK assembles into homodimers of ~95 kD subunit molecular mass. The monomer is comprised of three domains and contains two distinct reaction centers located ~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 domain motion of ~110° swivel 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 His-domain in the two conformational states of PPDK. His455 is shown in blue spheres:



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 from Clostridium symbiosum in the two extreme conformational states shown to the left 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. Note that the reaction pregresses in the movie in the reverse direction; steps 3 and 2 occur first followed by step 1. The movie was created by Kap Lim and osnat Herzberg


PPDK dimerPEP-binding domain - cyan; nucleotide binding domain - green; His-domain - yellow; domain linkers -red; phosphorylatable His455 - blue spheres
PPDK dimer
PEP-binding domain - cyan; nucleotide binding domain - green; His-domain - yellow; domain linkers -red; phosphorylatable His455 - blue spheres

Additional Resources

Larger movie frame for classroom projection
For additional information, see: Photosynthesis

Key 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.

3D Structures of PPDK

Updated June 2012

Pyruvate phosphate dikinase

2x0s – PPDK – Trypanosoma brucei
1kbl, 1dik – CsPPDK – Clostridium symbiosum
2dik, 1jde, 2r82 – CsPPDK (mutant)
2fm4 – CsPPDK phosphoryl-carrier domain - NMR
1vbg – mPPDK – maize
1ggo – PPDK (mutant) – Clostridium symbiosum

Pyruvate phosphate dikinase complex

1vbh – mPPDK + Mg + phosphoenolpyruvate
1kc7 - CsPPDK + Mg + phosphoenolpyruvate

Proteopedia Page Contributors and Editors (what is this?)

Osnat Herzberg, Michal Harel, Jaime Prilusky, Alexander Berchansky, Dan Bolser, Karl Oberholser, David Canner, Eran Hodis

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