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1: GLYCOLYSIS
14.1.1: INTRODUCTION
In this chapter, we will provide you with a historical overview of glycolysis and introduce you to the 10 enzymatic reactions in the pathway.
Our main goal is to understand how the oxidation of our major food molecules, sugars in the case of glycolysis, can lead to ATP synthesis.
Before we begin our journey into the glycolytic pathway, it is useful to review the concept of free energy within reactions. For a reaction to
be spontaneous, the change in the free energy within the system must be negative. From the equation in Figure 14.1.1 you can see that the
change in free energy of a reaction is dependent on concentration of the reactants and the products, as well as the temperature within the
system.
Figure 14.1.1 : The Change in Free Energy of a Reaction. The change in the free energy of a reaction is equal to the standard free
energy change for the reaction plus the gas constant (R) multiplied with the Temperature in Kelvin (T) and the natural log (ln) of the
concentrations of the products of the reaction (noted as C and D in the example) over the concentration of the reactants (noted as A and B in
the example).
You will note that some reactions of glycolysis and other metabolic pathways that we will investigate are not favored. Thus, it is necessary
to drive the reaction to become spontaneous by either coupling the reaction with a spontaneous reaction that can generate enough free
energy to drive the nonspontaneous reaction forward, or by using Le Chatelier’s principle and remove the products from the enzyme’s area
as soon as they are made. This will help drive the reaction in the forward direction as it will reestablish equilibrium. In this way, a small
amount of product can be formed spontaneously. Essentially, the continued removal of product or addition of excess reactant, will drive the
reaction forward. It is of note that the temperature of the reaction can also influence the change in free energy. However, in biological
systems, temperature changes that will significantly affect the change in free energy usually are not compatible with maintaining most life
forms. Thus, it will not be a large consideration in the context of our metabolic discussions, here.
When reactions are coupled together to obtain a spontaneous reaction, the overall free energy change for a chemically coupled series of
reactions is equal to the sum of the free energy changes of the individual steps, as noted in Figure 14.1.2 .
Figure 14.1.2 : The Coupling of Two Reactions. The top reaction is nonspontaneous with a positive change in free energy of 21 kJ/mol.
This reaction can be driven in the forward direction, by coupling it with a strongly spontaneous reaction that releases -34 kJ/mol. The
overall net reaction has a negative change in free energy and is spontaneous
The metabolic reactions of carbohydrates and other food molecules play an important role in generating energy within living systems in the
form of ATP. For carbohydrates, this begins with the metabolic process known as glycolysis (or the breakdown,’lysis’, of sugars, ‘glyco’) At
the end of the 1910s Otto Meyerhof mapped some of these metabolic conversions by measuring heat trends and oxygen consumption in frog
muscles. When the muscle is working, lactic acid is formed from carbohydrates, and Otto Meyerhof showed that during recovery, this is
followed partly by the burning of lactic acid and partly by reprocessing of lactic acid to carbohydrates.
Concurrently, Archibald Hill was also outlining these processes in the muscles of frogs. In opposition to the prevailing view that mechanical
movement and chemical processes were parallel sequences, Hill was able to show through measurements of heat generated by the
mechanical processes that these were delayed in relation to the movements. The chemical sequence consists of a work phase, which is not
dependent on oxygen supply, and a recovery phase, when oxygen is required. Together, their work has opened the door to understanding
aerobic and anaerobic metabolism beginning with the process of glycolysis. They both shared the Nobel Prize in Physiology and Medicine
in 1922 for their work in these processes Figure 14.1.3 .
14.1.1 https://bio.libretexts.org/@go/page/15004
Figure 14.1.3 : The Nobel Prize for Physiology and Medicine in 1922. Archibald V. Hill and Otto Fritz Meyerhof received this award
for their work on sugar metabolism and breakdown. Photos from Nobel Prize.Org
The glycolytic pathways consists of 10 enzymatic steps that convert glucose to pyruvate. This conversion generates a small amount of
energy. The pyruvate can then be converted to lactic acid (lactate) in vertebrates or to ethanol in yeast in an anaerobic (or oxygen-
independent) pathway or it can be fully oxidized to carbon dioxide in an aerobic (or oxygen-requiring) pathway that takes place within the
mitochondria (which is shown in green in Figure 14.1.4 : ). Aerobic oxidation yields about 18 times as much energy as the anaerobic
pathways causing them to be favored over anaerobic pathways. In fact, most animal tissues can only survive short anaerobic bursts that
occur in isolation and don’t involve the entire organism. The aerobic pathway is required to sustain life. Yeast also prefer to grow using the
aerobic, mitochondrial pathway. However, if oxygen is unavailable, yeast and other fungi can switch to anaerobic growth and produce
ethanol as a byproduct. The production of alcoholic beverages through this fermentation process is quite popular.
Figure 14.1.4 : Overview of Aerobic and Anaerobic Oxidation of Glucose. Figure modified from Kim, Y. et al (2011) PLoS ONE
6(12):e28293
Figure 14.1.5 provides a summary of the glycolytic pathway coupled to the oxidative phosphorylation pathway that occurs within the
mitochondria.
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Figure 14.1.5 : A Summary of the Glycolytic and Oxidative Phosphorylation Pathways. The glycolytic pathway is shown on the left
hand side in blue. During aerobic metabolism, pyruvate would be converted to acetyl-CoA where it would then enter into the Kreb cycle
within the matrix of the mitochondria. Future chapters will focus on the reactions inside the mitochondria. Our focus in this chapter will be
on the cytosolic reactions of the glycolytic pathway.
The major reactions of glycolysis are shown in Figure 14.1.6 . The pathway can be broken down into two major sections: (1) the energy
consuming reactions and the (2) energy generating reactions. People always say the old adage that ‘It takes money to make money’. The
same can be thought about the glycolytic pathway. The first section requires an investment of energy, in order to generate energy in the
second half of the reaction pathway. In this pathway, glucose, a 6 carbon hexose, is converted to two, 3C molecules - pyruvate. Note that
Figure 14.1.6 shows the entire pathway using Lewis wedge/dash representations plus the anaerobic conversion of pyruvate to lactate.
14.1.3 https://bio.libretexts.org/@go/page/15004
OH
O
glucose HO OH
HO OH
OH glyeraldehyde 3-phosphate -2
O3PO O
G3P
ATP
1. hexokinase NAD+ Pi
6. glyceraldehyde-3P
ADP
dehydrogenase
NADH + H+
CH2OPO3-2
HO O
O
glucose-6-P HO O
G6P HO OH
1,3-bisphosphoglycerate -2
O3PO O P O-
OH
1,3-BPG
-
O
2. phosphoglucose ADP
isomerase
-2 HO 7. phosphglycerate ATP
O3PO kinase
O 1
6 OH
fructose-6-P -2
OH 3-phosphoglycerate O3PO O
F6P
3PG
HO OH O -
ATP
3. phosphofructokinase 8. phosphglycerate
mutase
ADP
OPO3-2
-2
-2 O3PO HO O
O3PO 2-phosphoglycerate
O 1 2PG
fructose-1,6- 6
O-
bisP
F-1,6-BP OH
HO OH 9. enolase
H2O
-
4. aldolase -
O O
P
phosphoenol O O
O OH
-2 pyruvate PEP
O3PO OH -2
O3PO O O
1 -
glyeraldehyde 3-phosphate O
dihydroxyacetone phosphate G3P
DHAP ADP
5. triose phosphate 10. pyruvate
isomerase kinase
ATP
O O
pyruvate
C
lactate O
dehydrogenase
O- NADH
NAD+ + H+
HO O
lactate
Figure 14.1.6 : Glycolytic pathway. The chemical steps of the glycolytic pathway are shown using Lewis wedge/dash representations.
Enzymes required at each step are labeled in red. The energy consuming stage encompass reactions 1 - 3, whereas the energy producing
reactions occur in the second half of the pathway from reactions 4 - 10. The conversion of pyruvate to lactate by lactate dehydrogenase
represents anaerobic respiration as it occurs within mammalian species.
Glycolysis is the key anaerobic pathways for energy products in all organisms, except for lithotropes that use the oxidation of inorganic
molecules for energy production. In aerobic systems, glycolysis provides the release of fast energy within the body as glycogen metabolism
can quickly release free glucose for utilization. Given the centrality of glycolysis to all of life, we will explore each of the reactions in detail
below.
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OH CH2OPO3-2
ATP ADP
O O
HO HO
HO OH HO OH
OH 1. hexokinase OH
glucose-6-P
glucose G6P
NCBI iCn3D
Figure 14.1.8 : Yeast hexokinase PI in in the absence (2YHX) and presence (3B8A) of glucose. (Copyright; author via
source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...84YGEd1ob3th7A
Within Figure 14.1.8 , the gray structure is hexokinase without glucose (2YHX). However, it actually has a glucose analog bound, o-
tolyoylglucosamine (spacefill, yellow highlights), which apparently binds at the glucose binding site but does not cause a subsequent
conformation change. The cyan structures shows the enzyme with glucose shown as colored sticks. Note the large conformational change on
the actual binding of glucose, a classical example of an "induced fit" mechanism.
Figure 14.1.9 shows the surface of both enzymes using the same color coding as in the above figure These images better show how the
active site of hexokinase is occluded in the glucose-bound form. This prevents water access and hydrolysis of bound ATP instead of
"alcoholysis" of ATP (transfer of phosphate to glucose). The gray structure on left has the glucose analog bound which doesn't alter the
global conformation of the protein.
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Figure 14.1.9 : Surface of human hexokinase I with bound o-tolyoylglucosamine (spacefill, left, 2YHX) and with bound glucose
(spacefill, right, 3B8A)
Hexokinase I is the key form in the brain. It forms a complex with porin in the mitochondrial outer membrane and ATP/ADP translocase or
carrier protein in the mitochondrial inner membrane which facilitates the hexokinase reaction. The mechanism for the reaction of human
hexokinase I is shown in Figure 14.1.10 below.
H H
H O H
O O H
H Mg 2+
H
H O O
H H
ATP O-
- -
O R
N O P O- O
N Glucose
P O P O O H
H 2N O O O
N O
N O-
OH
HO H 2N NH2+ HO O
Arg 539
H H
H O H
O O H
H Mg 2+ O-
H - Glucose-6-P
H O O P
O O
-
H H O R
-
-
O O
N
N H
P O P O-
H 2N O O O O H
N O H
N O
OH
HO H 2N NH2+ HO O
ADP
HN 603Ser Asp 657
Arg 539
NCBI iCn3D
Figure 14.1.11 : Human hexokinase I with glucose and ADP in the active site (1dgk). (Copyright; author via source).
Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...aQy4gf6A2bWtp8
The key catalytic residue are shown in colored sticks and labeled. Glucose, ADP and PO42- are shown as colored spheres.
Note that hexokinase I, as well as forms II and III, have spatially distinct halves similar to those in the yeast enzymes. Forms I-III have a
molecule weight of about 100K. Form IV (glucokinase) has a molecular weight of 50K and is similar to the distinct halves of I-III.
suggesting that I-III arose through gene duplication.
Each half also binds glucose and ADP but the N-terminal of I and III are catalytically inactive. Hexokinase II, with both halves active, is the
main enzyme involved in glycolysis in most mammalian tissues. Other difference include that facts that glucose-6-phosphate, a product,
inhibits I-III. PO42- relieves G6P product inhibition in form I but not the others. ADP binding at multiple sites in hexokinase I likely causes
conformational change that affect structure and activity.
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14.1.3: SUGAR KINASES IN GENERAL
We will see many kinases that use ATP to phosphorylate sugars, so it useful to explore both their differences and similarities at the
beginning of our studies on carbohydrate metabolism.
Figure 14.1.12 below shows comparative structures of the five carbohydrate kinase classes.
Figure 14.1.12 : Structures of the five carbohydrate kinase classes. All images are shown in rainbow format (blue: N-terminus, red: C-
terminus). Roy, S.; Vivoli Vega, M.; Harmer, N.J. Carbohydrate Kinases: A Conserved Mechanism Across Differing Folds. Catalysts 2019,
9, 29. https://doi.org/10.3390/catal9010029. Creative Commons Attribution License
Panel (a) shows the structure of human glucokinase (hexokinase class; PDB (protein data bank) ID: 4IWV).
Panel (b) shows the structure of Bacillus subtilis fructokinase dimer: second molecule shown in raspberry (ROK kinase class; PDB ID:
1XC3 [17]).
Panel (c) shows the structure of Escherichia coli ribokinase (ribokinase class; PDB ID: 1RKD; [18]).
Panel (d) shows the structure of Aquifex aeolicus IspE (GHMP kinase class; PDB ID: 2V2Z; [19]).
Panel (e) shows the structure of human PIK3C3 (phosphatidylinositol phosphate kinase class; PDB ID: 3IHY).
ROK is bacterial Repressor, Open reading frame, Kinased are predominantly bacterial enzymes. Ribokinases include adenosine kinases,
fructokinases and phosphofructokinases. GHMP Kinases include Galactokinase, Homoserine kinase, Mevalonate kinase, and
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Phosphomevalonate kinase. Roy et al. Ibid
Many of these kinases are regulated by binding of allosteric effectors.
Figure 14.1.13 shows a common mechanism for all, using glucose as an example substrate.
this, hexokinasesare generally agreed to show a random sequential m
may bind rst [55]. Five conservedmotifs bind to the nucleotide, in
ts [54], which also coordinate an Mg2+ ion binding to the nucleotide
Figure 14.1.13 : Generic reaction mechanism for carbohydrate kinases (hexokinase shown). Roy et al, Ibid. The generic reaction is
initiated by a catalytic base abstracting a proton from the reactive hydroxyl (left). The oxygen atom then attacks the -phosphate of ATP
(second left), forming a pentacoordinate transition state (second right). This is stabilized by a divalent cation, and by the protein (not
shown). This transition state resolves leaving ADP and the phosphorylated carbohydrate (right).
HO H O CH2OH
CH2OPO3-2 2. phosphoglucose -2
O3PO
isomerase 1 O
6 O H OH
O HO H
HO glucose-6-P HO H fructose-6-P
OH H OH
HO OH G6P H OH F6P
OH 2. PHOSPHOGLUCOSE H OH O
HO OH H OH O ISOMERASE
H2C O P O
glucose-6-P H2C O P O
G6P fructose-6-P O
O
F6P
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Lys 518
Lys 518
Lys 518
O O-
O O- P
P -
-
O O NH2
O O NH2
H OH
O HO O-
HO OH
HO O H
HO O H H
O His388
H His388
O- N+
N+
O
O HN
HN
Glu357
Glu357
Lys 518
O O-
P
-
O O NH3+
O
HO OH
HO OH
O - His388
N
O
HN
Glu357
Figure 14.1.15 : Mechanism for phosphoglucose isomerase. Ribeiro AJM et al. Ibid
Figure 14.1.16 below shows an interactive iCn3D model of rabbit phosphoglucose isomerase with bound 6-phosphogluconic acid
(1DQR)
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NCBI iCn3D
Figure 14.1.16 : Rabbit phosphoglucose isomerase with bound 6-phosphogluconic acid (1DQR). (Copyright; author via
source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...xo1SgF1ZpAySm9
One monomer of the dimer is shown in gray and the other in cyan. The catalytic residues Lys518 and His388 are shown in both subunits in
colored sticks and labeled. Additional residues that contribute to specificity (Ser209, Ser159, Thr214, Thr217, and Thr211) are shown in the
gray subunit with color sticks and labeled. 6-phosphogluconic acid, a competitive inhibitor, is shown in color spacefill.
The enzyme also has other functions in addition to its role in glycolysis, so it is a member of a group called "moonlighting" (a term that
refers to working at a secondary job). proteins. Outside of the cell, phosphogluco isomerase acts as a nerve growth factor and cytokine. It is
also called autocrine motility factor (PGI/AMF) and its cytokine activity is associated with aggresive cancers.
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-2 HO -2
O3PO
O3PO -2
O3PO
O 1 ATP 1
6 ADP O
6
OH OH
3. phosphofructokinase
HO OH HO OH
fructose-6-P fructose-1,6-bisP
F6P F-1,6-BP
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Arg72
Arg171
-
O NH
O- R Gly11
O P +
H2 N NH2
O NH O HN R
F6P O
+
H2 N NH2
Thr125
OH
HO HO
O O-
OH H O P O O O HO
P OH
O- O- ATP
-
O H O P O
O O-
O H O N
H N
Mg2+ O
Asp127 - H N
O
O O NH2
H O O- N
H
Asp129 Asp103
-
O
O-
O P
O F-1,6-BP
O
OH
HO ADP
O O
OH P - HO O HO
H H -
O O P O OH
O H
O O- O P O
H -
O O O
O H N N
H Mg2+ O
Asp127 - H N
O
O O NH2
H O O- N
H
Asp129 Asp103
-
O
O-
O P
O
O F1,6-BP
OH
HO O ADP
O
OH P - HO O HO
H H -
O O P O OH
O+ -
O O- O P O
H H
O O- O
O H N N
H Mg 2+ O
Asp127 - H N
O
O O NH2
H O O- N
H
Asp129 Asp103
Figure 14.1.18 : Proposed mechanism for E. Coli phosphofructokinase. Ribeiro AJM et al. Ibid
Figure 14.1.19 below shows an interactive iCn3D model of the E. Coli phosphofructokinase with bound F1,6-bisphosphate and ADP
products (1PFK). (long load)
14.1.12 https://bio.libretexts.org/@go/page/15004
NCBI iCn3D
Figure 14.1.19 : E. Coli phosphofructokinase with bound F1,6-bisphosphate and ADP products (1PFK). (Copyright;
author via source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...t4KKgLAGzHrzo8
Each monomer of the tetramer is shown in a different color. The gray monomers shows key binding and catalytic residues described in the
mechanism above. F1,6-bisphosphate is shown as spacefill and ADP is shown as sticks.
The structure of the human platelet PFK1 tetramer has been determined in the presence of ATP and ADP. Figure 14.1.20 below shows an
interactive iCn3D model of the human phosphofructokinase-1 dimer (for clarity) in complex with ATP and Mg (4XYJ). (long load)
NCBI iCn3D
Figure 14.1.20 : Human phosphofructokinase-1 dimer in complex with ATP and Mg (4XYJ). (Copyright; author via
source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...AKfonyGsNq6Cs9 (long load). Here is a
link to the ADP bound structure: https://structure.ncbi.nlm.nih.gov/i...N81MBS4PZfSQp9
The monomers are shown in colored surface with secondary structure underneath. Note that side chains from each monomer in the dimer
contribute to binding and catalysis. The actual PDB structure is tetrameric. The structures have an E173S mutation.
Figure 14.1.21 shows the differences in orientation of the key side chains in the ADP structure (left) and the ATP structure (right) that are
key in the conformation changes in the enzyme on binding substrate.
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ADP bound form of human PFK (4XKJ) ADP bound form of human PFK (4XYJ)
Figure 14.1.21 : Conformation changes in the active site of PFK on ATP hydrolysis
O
CH2O P O
O H
O O O
HO H O3PO C CH2OH
fructose-1,6-bisP H2 + H OH
H OH
F-1,6-BP 4. ALDOLASE CH2OPO3
H OH O
H2C O P O
O dihydroxyacetone phosphate glyceraldehyde-3-P
DHAP G3P
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| y g y
I Higher eukaryotes (plants, animals), some • Mechanism of action: Schiff base forms
protozoans (e.g., Trypanosoma brucei, Leishmania substrate intermediate
donovani, Plasmodium falciparum), some bacteria, • Structure: Typically forms homo-tetramers,
some algae contains TPI β/α-barrel fold
IA Archaea • Mechanism of action: Schiff base forms
substrate intermediate
• Structure: Typically forms homo-octamers/
decamers/higher oligomers, contains TPI
β/α-barrel fold
II “Lower” eukaryotes (some protozoans (e.g., • Mechanism of action: Divalent ion forms
Giardia lamblia), fungi, yeasts, algae), most substrate intermediate, metal-dependent
bacteria, some archaea • Structure: Typically forms homo-dimers,
contains TPI β/α-barrel fold
Class I Aldolase
These enzymes proceed through a Schiff base intermediate between a reactive lysine and and the reactant/product. The enzyme is favored in
the reverse direction and its perhaps easier to see the mechanism presented in that fashion. In rabbits, the muscle Class I aldolase (RAMA)
uses Lys-229 to form a Schiff base with DHAP as shown in a mechanism presented in Figure 14.1.23 below.
F1,6-BP
DHAP -
- O O OH
O 1 2 3
P -2
O3PO 3 5 6
O OH 2 OPO3-2
O 4
O 1
OH OH
Enz-Lys-NH 2 Enz-Lys-NH 2
B:
Lys
Arg
NH Enz
- +
HN H O
O OH H2
N+ P
O- 1 2 3 H N
H N H O
6
H C 5
O 4 OPO3-2
B H OH G3P
Figure 14.1.23 : Class I aldolases - general mechanism (after Bolt et al., Arch Biochem Biophys. 2008 June 15; 474(2): 318–330)
Only the pro(S) proton of the dihydroxyacetone phosphate C3 carbon is removed and effectively exchanged with the glyceraldehyde-3-
phosphate substrate. Figure 14.1.24 below reviews how the pro(R) and pro(S) hydrogens can be visually differentiated by replacing one
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with a deuterium and determining the stereochemistry of the now chiral C3.
DHAP
-
-
O
O D H - O- H D
1 2 O 1 2
P P
O (R) OH O (S) OH
O 3 O 3
O O
DHAP
-
Ser300 OH O O
OH O
O Tyr 363
O- H
O
NH2 P
O O H
O- H
Lys 229 H NH2
O O
NCBI iCn3D
Figure 14.1.21 : Dihydroxyacetone phosphate enamine intermediate in fructose-1,6-bisphosphate aldolase from rabbit muscle
(2QUT). (Copyright; author via source). Click the image for a popup or use this external link:
https://structure.ncbi.nlm.nih.gov/i...uR5KZBsfN8QQh9
Only one monomer of the four in the homotetramer is shown. The ligand, 1,3-dihydroxyacetonephosphate, is shown in spacefill with CPK
colors. It is Schiff base linkage with Lys229. The key catalytic residues are shown and labeled.
The reaction proceeds between eneamine and iminium covalent intermediates. A K146M mutation (in the active site) decreases enzyme
activity and allows trapping of the K229 eneamine intermediate. A key tyrosine (Y363) in its deprotonated state formed in the presence of
the iminium phosphate and a local water appears to abstract the C3 pro(S) proton to form the enamine.
Class II Aldolase
Figure 14.1.22 :
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O
O
Glu O- F1,6-BP
Glu O-
O-
- H O HO
O
1 2
P C3 -2
O3PO 3 5
O OH 2 4 6 OPO3-2
O 1
O OH OH
DHAP Zn2+
O O
H
Glu O Glu O
H OH G3P
O 4 -6 OPO3-2
C
- O- H O-
O 1 2 6 - 3
P C3 C 5 O
P
1
2 CH
O OH O 4 OPO3-2 O
O O O
O- OH G3P O
Zn2+ Zn2+
enediolate
Figure 14.1.22 : Class II aldolases - general mechanism (after Bolt et al, ibid)
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Figure 14.1.24 : Proposed mechanism for triose phosphate isomerase (after Bolt et al, ibid)
Note that the reaction employees the deprotonation of a neutral imidazole side chain to form an imidazolate anion. This would not likely to
be favorable, given its pKa value.
The are four possible conserved proton donors with more reasonable pKas in the active sites of TPIs, including K12, H95, E97 and E165.
Mutations of E97 to E97Q and E97D lead to a 4000-fold reduction in kcat (E97Q) but only a 100-fold reduction for E97D suggesting that
E97 is the key general acid/base.
Figure 14.1.25 below shows an interactive iCn3D model of the chicken triosephosphate isomerase-phosphoglycolohydroxamate complex
(1TPH)
NCBI iCn3D
Figure 14.1.25 : Chicken triosephosphate isomerase-phosphoglycolohydroxamate complex (1TPH) . (Copyright; author via
source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...AFXpt9kg5aki5A
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The four key conserved residues are shown in the gray monomer of the homodimer.
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Figure 14.1.27 : Proposed mechanism for glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi (after Reis et al. Phys.Chem.
Chem. Phys., 2013, 15, 3772. https://pubmed.ncbi.nlm.nih.gov/23389436/)
The reaction proceeds in two parts. The first (top section) is the oxidation of glyceraldehyde-3-phosphate (G3P) by NAD+ to the state of a
thioester attached to Cys166. The now reduced NADH dissociates, and is replaced by a new NAD+ for another cycle of catalysis. In the
meantime, inorganic phosphate, Pi, binds and reacts with the thioester to form 1,3-bisphosphoglycerate (1,3-BPG).
The mechanism is not entirely clear. There are two phosphate binding sites, Pi (red) and Ps (purple) which interact with phosphate groups
on the substrates. The oxidation part of the reactions appears to take place at the Pi site. Ps is composed of the side chains of Thr197,
Thr199 and the 2-hydroxyl group of the ribose in NAD+. Pi site seems more variable but in the T. cruzi enzyme appears to consist of Thr226
and Arg249, Gly227, Ser 247. The mechanism appears to involve a flip of orientation of substrates and intermediates after the dissociation
NADH from the enzyme.
Figure 14.1.28 below shows an interactive iCn3D model of the Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase with bound
NAD and a 1,3-bisphosphoglycerate analogue (1QXS)
NCBI iCn3D
Figure 14.1.28 : Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase with bound NAD and a 1,3-
bisphosphoglycerate analogue (1QXS) . (Copyright; author via source). Click the image for a popup or use this external link:
https://structure.ncbi.nlm.nih.gov/i...WnsNSgmA3AJyw6
Only two monomers of the homotetramer are shown for clarity. The Pi site is shown in magenta and the Ps site in purple. The phosphonic
acid analog is shown in spacefill and NAD in sticks. The active site His194 and Cys166 are also shown in sticks and labeled.
14.1.9: REACTION 7: 1,3 BPG + ADP + H+ → 3PG + ATP ΔGO= -4.5 KCAL/MOL
This reaction, catalyzed by phosphoglycerate kinase, is shown in Figure 14.1.29 below
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Figure 14.1.30 : Reaction mechanism for phosphoglycerate kinase
Figure 14.1.31 below shows an interactive iCn3D model of human phosphoglycerate kinase in complex with ADP, 3PG and magnesium
trifluoride (2WZB).
NCBI iCn3D
Figure 14.1.31 : Human phosphoglycerate kinase in complex with ADP, 3PG and magnesium trifluoride (2WZB). (Copyright;
author via source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...w5yvu2VuGhmQXA
3-phosphoglycerate is shown in spacefill with CPK colors. ADP plus the adjacent MgF3 is a mimetic for the transition state for ATP
synthesis. Hence this structure shows the products/transition state in a closed active site, which as we have seen before prevents spurious
hydrolysis of 1,3-BPG or ATP.
Figure 14.1.32 below shows an interactive iCn3D model of the alignment of the open form of human phosphoglycerate kinase (2XE7) with
bound 3PG and ADP with the closed form with bound 3PG, ADP, and MgF3 (2WZB).
NCBI iCn3D
Figure 14.1.32 : Alignment of the open form of human phosphoglycerate kinase (2XE7) with bound 3PG and ADP with the
closed form with bound 3PG, ADP, and MgF3 (2WZB). (Copyright; author via source). Click the image for a popup or use this external
link: https://structure.ncbi.nlm.nih.gov/i...n5FfsJeYitiWr9
Use the "a" key to toggle back between the open form (magenta) and closed forms (cyan). In the closed state most closely representing the
bond transition state of ATP, the two lobes of the enzyme clamp together.
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This isomerization reaction proceeds with little thermodynamic barrier. It's function is to locate the phosphate on C2 which on the next
reaction (dehydration) will form a molecule whose phosphoryl transfer potential is greater than ATP. It's seems so simple but the enzymes
that catalyse this reaction are diverse and quite complicated from a mechanistic perspective.
There are two types of PGMs, bisphosphoglycerate and monophosphoglycerate mutases that carry out three different reactions involving
shuffling of phosphates from one position to another in 3C sugars or cleavage of a phosphate from a sugar
3-phosphoglycerate ↔ 2-phosphoglycerate (reaction 8 of glycolysis) catalyzed by bisphosphoglycerate and monophosphoglycerate (the
glycolytic enzyme) mutases
1,3-bisphosphoglycerate ↔ 2,3-bisphosphoglycerate by bisphosphoglycerate mutases
2,3-phosphoglycerate ↔ 3-phosphoglycerate + Pi by bisphosphoglycerate mutases
Within the monophosphoglcyerate mutases, and more specifically the phosphoglycerate mutase (PGM) of glycolysis, there are two types
one that depends on the cofactor 2,3-phosphoglycerate. These are called cofactor-dependent phosphoglycerate mutase (dPGM) and are
found in mammals, yeast and some bacteria. They do not require metal ions.
one that does not depend on the cofactor 2,3-phosphoglycerate. These are called cofactor-independent phosphoglycerate mutase (iPGM)
and are found in plants and some bacteria. These can only interconvert 3PGA and 2PGA. One family of enzymes in the class requires
Mn2+ while the other requires Mg2+ or Zn2+. These enzyme are often structurally similar to alkaline phosphatases
The cofactor-independent and cofactor-dependent monophosphoglycerates (such as the phosphoglycerate mutase of glycolysis) are very
different structurally and mechanistically so we will look at both types of mechanisms. With each type the enzyme sequences are very
conserved.
Mechanism of cofactor (2,3-BPG) dependent phosphoglycerate mutase (dPGM)
The reaction is much less complicated than the cofactor independent PGM. It involves the transfer for the phosphate on the C3-OH to a the
nucleophilic nitrogen on histidine (His8) in the active site to form a covalent pHis8 intermediate. A proximal Glu86 presumably acts as
general acid to donate a protein to the dephosphorylated O on C3 of the substrate. An active site arginine (Arg 59) would stabilized the p-
His intermediate and its transition states. The phosphate on pHis could then be transferred to the O on carbon C2 of the substrate.
Figure 14.1.34 below shows an interactive iCn3D model of yeast phosphoglycerate mutase (cofactor dependent) bound to 3-
phosphoglycerate (1QHF)
NCBI iCn3D
Figure 14.1.34 : Yeast phosphoglycerate mutase (cofactor dependent) bound to 3-phosphoglycerte (1QHF). (Copyright; author
via source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...9F4oc6mmr5DFs9
Mechanism of cofactor independent phospoglycerate mutase (iPGM)
Let's consider the mechanism for the Mn2+-requiring iPGM from Geobacillus stearothermophilus. Two Mn2+ ions are in the active site. The
mechanism for the first half of the cofactor independent phosphoglycerate mutase (iPGM) reaction is shown in Figure 14.1.35 below.
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Figure 14.1.35 : Part A - Mechanism for cofactor independent phosphoglycerate mutase (iPGM) from Geobacillus stearothermophilus (after
Bolt et al, ibid)
Arg 261 interacts with the substrate, stabilizing the negative charge in it and in its transition state. It also makes the target phosphorous more
electrophilic. Ser62 is activated by a Mn2+ ion to become more nucleophilic on abstraction of a proton by Lys336. Reaction 3 probably
proceeds through an SN2 mechanism.
The rest of the mechanism is shown in Figure 14.1.36 below.
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Figure 14.1.36 : Part B - Mechanism for cofactor independent phosphoglycerate mutase (iPGM) from Geobacillus stearothermophilus (after
Bolt et al, ibid)
The iPGMs are monomers with two distinct domains (lobes) containing a substrate binding site separated from an active site. They are
connected by flexible sequence than bend to produce either an open or closed form of the enzymes (as we have seen before). In some
enzymes the two sites are merged at the interface between the domain. The active site Ser62 becomes phosphorylated and then transfers its
phosphate to the new site in the substrate which is oriented differently in the enzyme.
Figure 14.1.37 below shows an interactive iCn3D model of the Geobacillus stearothermophilus cofactor-Independent Phosphoglycerate
Mutase (iPGM) with bound 2-phosphoglycerate (product) (1O98)
NCBI iCn3D
Figure 14.1.37 : Cofactor-Independent Phosphoglycerate Mutase with bound 2-phosphoglycerate (product) (1O98) .
(Copyright; author via source). Click the image for a popup or use this external link:
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https://structure.ncbi.nlm.nih.gov/i...71iYHXAEKMGsEA
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NCBI iCn3D
Figure 14.1.40 : Yeast enolase with bound 2-phosphoglycerate (7ENL) . (Copyright; author via source). Click the image for a
popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...TgwYV9vF8cYtPA
14.1.12: REACTION 10: PEP + ADP → PYR + ATP ΔGO= -7.5 KCAL/MOL
This reaction, catalyzed by pyruvate kinase, is shown in Figure 14.1.41 below
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NCBI iCn3D
Figure 14.1.43 : Rabbit muscle pyruvate kinase complexed with Mn2+, K+, and pyruvate (1PKN). (Copyright; author via
source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...cZkm8DdEw2N3C6
We are done! Given that glycolysis is the central anaerobic energy extracting pathway in all life, it is important that we examined each
enzyme in detail.
This is the net reaction of the glycolytic pathway:
+ +
Glc + Pi + 2 ADP + 2 NAD ⟶ 2 Pyr + 2 ATP + 2 NADH + 2 H + 2 H2 O
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Figure 14.1.44 : Oxidation and substrate-level phosphorylation in glyceraldehyde-3-phosphate dehydrogenase (after Voet and Voet)
Summary: Under anaerobic conditions, glucose (6Cs) is metabolized through glycolysis which converts it to two molecules of pyruvate
(3Cs). Only one oxidation step has been performed when glyceraldehyde 3-phospate is oxidized to 1,3-bisphosphoglycerate. To regenerate
NAD+ so glycolysis can continue, pyruvate is reduced to lactate, catalyzed by lactate dehydrogenase. These reactions take place in the
cytoplasm of cells actively engaged in anaerobic oxidation of glucose (muscle cells for examples during sprints). Note that the enzyme is
named for the reverse reaction, the oxidation of lactate by NAD+. This reaction is shown in Figure 14.1.45 below.
This page titled 14.1: Glycolysis is shared under a not declared license and was authored, remixed, and/or curated by Henry Jakubowski and Patricia Flatt.
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