Glycerate Kinase Information

Enzyme Name

Glycerate Kinase

Reaction Catalyzed

Group Transfer from 1,3 bisphosphoglycerate to ADP to make ATP

Reaction Type

Rationale

A group transfer of phosphate onto ADP to make ATP is made thermodynamically favorable even starting from the standard state because the phosphate is coming off of an organic acid. Please recall a couple modules ago, a quiz question dealt with the Free Energies of a phosphate hydrolysis from two different functional groups: 1. an alcohol, 2. an organic acid; the Standard Free Energies differed substantially at -17 kJ/M and -42 kJ/M respectively.  This will be described in more detail in later pages of this module, but the energy of hydrolysis can be linked to another reaction (in this case the transfer of a phosphate onto ADP to make ATP). In terms of thermodynamics, these two reactions can be considered as individual half reactions and can be combined into a single overall reaction such that the favorable Free Energy of one "half reaction" can be used to counteract the unfavorable Free Energy of another. In this case

Pathway Involvement

Glycolysis AND gluconeogenesis

Cofactors/Cosubstrates

ADP is a cosubstrate in glycolysis direction and ATP is a coproduct

DG^o'

-18.9 kJ/M

Starting from standard state and allowing the reaction to come to equilibrium the 3-Phosphoglycerate and ATP concentration would end up ~200 times higher than the product of the concetrations of 1,3bisPhosphoglycerrate and ADP.

The Standard Free Energy favors ATP production - the reason for this is outlined above.

K_eq

Comments

For each glucose that started glycolysis there are two glycerates. so 2 ATP are made for each of these reactions.

Our total ATP for glycolysis is now even. It took two ATP to get the pathway started (1 for hexokinase, 1 for phosphofructokinase-1). Now those two ATP have been returned. In terms of what the organism needs most.. energy transfer from sugar to ATP we are now even.

"In cell" Substrate Concentrations^*

S₁ =

S₂ =

P₁ =

P₂ =

ATP

1.85 mM

DG for these conditions

+0.1 kJ/M

Mechanism for Chemistry

Mechanism for Enzyme

Picture of Enzyme with substrate

1. RibbonsAldolase. Here only the main chain is represented by these ribbons. There are four identical subunit
2. one subunit with substrate Three of the subunit deleted and a substrate analog (mannitol-1,6-bisphosphate) is added in the atom colored spheres. C=Gray; O=red; P=Orange. three critical AA in the active site are also added.
3. as above closeupSame picture as in "2" but zoomed in
4. substrate rotationas in "3" ribbons deleted and allowed to rotate to show the orientaion of these 3 amino acids. A.) LYS near C2 - this will form the Schiff's base; B.) GLU near C2 - will help the Schiff's base form by "attracting the water" as the Schiff's base forms; C.) LYS near C4 - will help the hydroxyl group deprotonate as the aldol reaction begins.
5. substrate and all nearby AAAll amino acid sidechains near the mannital are turn on
6. Schiff's base LYS in cyan and near GLU in yellow The LYS that will form the Schiff's base is color cyan, C2 of mannitol is colored magenta and the GLU is color yellow. The roles are highlighted in "4"
7. LYS near and near C_{4/sub> in cyan The LYS near C4 is colored cyan, C4 of mannitol is color magenta.}