Pyruvate phosphate dikinase: Difference between revisions

==Pyruvate Phosphate Dikinase - a Molecular Machine==

'''Pyruvate phosphate dikinase''' (PPDK) is an enzyme that catalyzes the inter-conversion of adenosine triphosphate (ATP), phosphate (P_i), and pyruvate with adenine monophosphate (AMP), pyrophosphate (PP_i), 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:

[[Image:1KBL dimer.png|left|150px|''PPDK dimer'']]<br />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.

<br>PEP-binding domain - cyan; nucleotide binding domain - green; His-domain - yellow; domain linkers -red; phosphorylatable His455 - blue spheres|200px]]

'''''The movie''' depicts the catalytic reaction involving 3 in-line phosphotransfers & the accompanied protein conformational transitions. Model based on crystal structures of PPDK from '''Clostridium symbiosum''' in the 2 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 & blue, PEP binding domain colored cyan, His-domain colored yellow, and linker segments that connect the His-domain to the partner domains colored red. Ligands and the catalytic histidine are depicted in stick models with the atomic color scheme: '''''C''''' – gray, '''''N''''' – blue, '''''O''''' – red, '''''P''''' – green, '''''Mg''''' – magenta. Note that the reaction progresses 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''<br>

<br>You may also [http://youtu.be/hxuBouGfs_4 download] the full High Resolution video.

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==Additional Resources==

[[User:Karl_Oberholser/PPDK_large|Larger movie frame]] for classroom projection <br>

*Pyruvate phosphate dikinase

**[[2x0s]] – PPDK – ''Trypanosoma brucei''<br />

**[[1kbl]], [[1dik]] – CsPPDK – ''Clostridium symbiosum''<br />

**[[2fm4]] – CsPPDK phosphoryl-carrier domain - NMR<br />

*Pyruvate phosphate dikinase complex

**[[1vbh]] – mPPDK + Mg + PEP<br />

**[[5jvj]], [[5jvn]] - cyPPDK + Mg + PEP - clustered yellowtop<br />

**[[5jvl]] - cyPPDK + Mg + PEP + ATP analog<br />

**[[5lu4]] - cyPPDK + Mg + ADP + pyruvate<br />

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