15.2: Glycogenesis
- Page ID
- 15014
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(Learning goals written by Claude, Sonnet 4.6, Anthropic)
Enzymes of Glycogen Synthesis: Reactions and Mechanisms
- Describe the sequential roles of hexokinase, phosphoglucomutase, UDP-glucose pyrophosphorylase (UGPase), glycogenin, glycogen synthase, and the glycogen branching enzyme in converting free glucose to a mature, branched glycogen polymer, identifying the bond formed or broken and the energy source at each step.
- Explain the mechanism of UGPase, including the sequential bi-bi kinetic mechanism, the role of Mg²⁺ in positioning substrates for nucleophilic attack of glucose-1-phosphate on the α-phosphorus of UTP, and the significance of pyrophosphate release in driving the reaction forward.
- Describe the autoglucosylation reaction of glycogenin, including the roles of Tyr-194, Mn²⁺, and conserved aspartate residues in initiating the glycogen primer, and explain why a primer is required for glycogen synthase activity.
- Explain how glycogen synthase extends the α1→4 main chain using UDP-glucose as the activated glucosyl donor, and explain why a separate branching enzyme is required to introduce α1→6 linkages, describing the transglycosylation mechanism of the glycogen branching enzyme and the physiological advantage of branching.
Structural Basis of Glycogenin–Glycogen Synthase Cooperation
- Describe the three conformational states (closed/inactive, partially open, and open/active) of the glycogenin–glycogen synthase complex, and explain how allosteric transitions between these states coordinate the handoff of the glycogen primer from glycogenin to glycogen synthase for chain elongation.
- Explain how glucose-6-phosphate binding to glycogen synthase drives a T-to-R-like conformational transition that opens all four active sites of the tetramer simultaneously, connecting this structural change to the enzyme's allosteric activation.
Regulation of Glycogen Synthase Activity
- Describe the multi-site phosphorylation of glycogen synthase — including the role of the arginine cradle in stabilizing the inactive T state through electrostatic interactions with pSer641 — and explain how hierarchical phosphorylation creates a hyperphosphorylated "spike" that locks the enzyme in an inactive conformation.
- Integrate the regulatory mechanisms of glycogen synthase — allosteric activation by glucose-6-phosphate, inactivation by phosphorylation via GSK-3, and reactivation by PP1-mediated dephosphorylation — into the broader context of insulin signaling and fed-state glucose metabolism, explaining how these mechanisms ensure glycogen is synthesized when glucose is abundant.
Introduction
The process of forming glycogen is called glycogenesis, and it requires the activity of six enzymes, as illustrated in Figure \(\PageIndex{1}\). We have already discussed several, including hexokinase, which phosphorylates the 6'-OH of glucose, and phosphoglucomutase, which converts glucose-6-phosphate to the glucose-1-phosphate isomer. This section discusses the remaining four enzymes and their roles in glycogen biosynthesis. They are Glycogen Synthase, UDP-Glucose Pyrophosphorylase (preferred name UTP-glucose-1-phosphate uridylyltransferase), glycogenin, and glycogen branching enzyme.
Given their importance in synthesizing the second main energy storage molecule, we must probe them in detail.
Glycogen synthase (GS) is a key enzyme whose activity is highly regulated. In Chapter 15.1, we have already explored how insulin signaling upregulates the activity of this enzyme by inhibiting GSK-3-mediated phosphorylation. Other effectors include allosteric binding of glucose-6-phosphate, which also increases GS activity. In a later section, we will also see that the hormone glucagon can regulate GS activity through protein kinase A (PKA), decreasing glycogen synthesis and increasing glycogen breakdown.
In the glycogenesis pathway, GS is responsible for forming most of the α1→4 glucose acetal linkages. The GS requires a primer of 4-6 glucose residues linked together by α1→4 bonds to initiate synthesis. Since GS can only form α1→4 linkages in the main chain, it CANNOT create the α1→6 branches inherent to the core structure of glycogen.
GS uses the glycogen primer and glucose, activated by covalent attachment to uridine diphosphate (UDP) at the 1-position, to build the glycogen main chain. Upon completion of one round of synthesis, the 1 position of the incoming UDP-glucose is covalently attached to the 4 position of the nascent glycogen molecule, releasing UDP as the leaving group.
\[\text { Glycogen }_{(n)}+\text { UDP-glucose } \rightarrow \text { Glycogen }_{(n+1)}+\text { UDP } \nonumber \]
UTP--glucose-1-phosphate uridylyltransferase (or UDP-Glucose Pyrophosphorylase)
The formation of the UDP-glucose required for the synthesis of the main chain of glycogen is mediated by UTP-glucose-1-phosphate uridylyltransferase (preferred name), which is also called UDP-glucose pyrophosphorylase (GalU or UGPase; EC 2.7.7.9). UGPase catalyzes the reversible reaction of glucose 1-phosphate and UTP into UDP-glucose and inorganic pyrophosphate (PPi) (Figure \(\PageIndex{2}\)). Enzymes of the UGPase family are ubiquitous and can be found in the tree of life.
UDP-glucose is an activated form of glucose used to synthesize other glycans, including sucrose, cellulose, starch, and glycogen, and the glycan parts of glycoproteins, glycolipids, and proteoglycans. Hence, it is a key metabolite that underscores the importance of understanding UGPase.
Like many other nucleotidyl transferases, UGPase requires divalent cations to promote the reaction (Figure \(\PageIndex{3}\)). In most cases, magnesium ions are employed. The reaction mechanism follows a sequential bi-bi-mechanism, starting with the binding of UTP to the active site in the presence of a magnesium ion, followed by the binding of glucose 1-phosphate. The octahedral coordination sphere of magnesium positions the substrates correctly and enables the nucleophilic attack of glucose 1-phosphate on UTP. A lysine, an aspartate, and several water molecules within the active site help stabilize the position of the substrates and cofactor for the proper nucleophilic attack of the phosphoryl oxygen of glucose 1-phosphate on the α-phosphorus atom of UTP. Finally, PPi is released from the UGPase/Mg2+/UDP-glucose complex. UDP-Glucose then dissociates from the complex, restoring the enzyme's active site for another round of synthesis.
Figure \(\PageIndex{4}\) shows an interactive iCn3D model of the human UDP-glucose pyrophosphorylase tetramer (3R2W).
Figure \(\PageIndex{4}\): Human UDP-glucose pyrophosphorylase tetramer (3R2W). (Copyright; author via source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/icn3d/share.html?9yq9STPGvq87Wnbt8
Substrate binding residues and the active site are shown as CPK-colored sticks, labeled in one of the subunits. Three key loops whose correct positioning is required for catalysis are colored as follows:
- Latch Loop: 406-416, yellow, which contains Glu 412 (shown in spacefill)
- SB Loop: 275-282, red
- 309 Loop: 309-311, cyan, which contains Ser 309 (shown in spacefill).
For clarity, only four of the eight subunits are shown. Note the proximity of the interacting loops positioned between the brown and magenta subunits. The SB and 309 loops at that location are part of the brown subunit, while the yellow latch loop is part of the magenta subunit. The latch loop is between the SB and 309 loops. The cyan 309 loop is prevented from interacting with the substrate and the movements of the SB and 309 loops needed for catalysis. In other species, the SB loop has been observed to move down to bind UDP-glucose at the active site. The structure above represents the apo-enzyme, which is inactive and in its closed form without a bound substrate.
Mutations in the 309 loop (S309N/S311R) still had 84% of normal activity. Glu412 in the latch loop is highly conserved in vertebrates (but not in yeast). Mutations at Glu 412 didn't affect the formation of enzyme oligomers but did affect activity.
- replacing E412 with a short aspartate (E412D) significantly increases activity (176%)
- E412Q, which eliminates the charge while retaining the approximate size of the side chain, showed just a marginal increase in activity (19%)
- E412K, which flips the charge and extends the side chain, decreased activity to 22%.
These mutations generally suggest that steric effects in the region of subunit interaction are most important in activity.
Glycogen Synthase
UDP-glucose is then utilized by glycogen synthase (GS) to extend the main chain of glycogen by one glucose residue. In this reaction, the 4’-OH group of the glycogen main chain attacks the anomeric carbon of UDP-glucose (Figure \(\PageIndex{5}\)). The UDP functional group is a good leaving group, facilitating the formation of the α1→4 bond.
Glycogen synthase has two isoforms: GS1, expressed in tissues that contain glycogen (e.g., muscle), and GS2, expressed only in the liver. We will explore its mechanism more fully below.
Glycogenin
Previously, we mentioned that GS requires a glycogen primer of 4 – 6 glucose residues to add new residues to the main chain. The small docking protein, Glycogenin (GN or GYG), provides this primer. This protein is a homodimer that self-catalyzes its own glycosylation at amino acid Tyr-194. In this reaction, UDP-glucose is coordinated by a Mn2+ metal cofactor and critical aspartate residues (Figure \(\PageIndex{6}\)). The –OH group of Tyr-194 then mediates nucleophilic attack on the anomeric carbon of UDP-glucose. Thus, glycogenin is tethered to the reducing end of the glycogen molecule.
As with glycogen synthase, glycogenin (GN or GYG) has two isoforms, with GN2 (or GYG2) mainly expressed in the liver, pancreas, and heart.
Mechanisms for glycogen synthesis by glycogenin and glycogen synthase
How do glycogenin and glycogen synthase cooperate in the synthesis of glycogen? Structures of the complex of glycogenin-1 (GYG1), which seeds the molecule by starting glycogen synthesis by autoglucosylation, and glycogen synthase-1 (GS1 or GYS1), which extends the molecule, show allosteric transitions between three primary states, the closed/inactive, partially open, and open active complex, as shown in Figure \(\PageIndex{7}\):
Figure \(\PageIndex{7}\): GYS1 chains A, B, C, and D are colored orange, turquoise, purple, and navy, respectively. GYG1 globular domains and the GYG1-tail fragment are colored in gray shades for all chains. The bottom left structure shows the apo GYS1:GYG1 mobile complex. The bottom middle structure is the apo GYS1:GYG1 ordered complex. The bottom right structure is the +G6P GYG1:GYS1 complex. Fastman et al., 2022, Cell Reports 40, 111041 July 5, 2022, 2022. https://doi.org/10.1016/j.celrep.2022.111041. Creative Commons Attribution (CC BY 4.0)
It makes sense that both enzymes bind to each other and cooperate in the synthesis of glycogen. In the closed state, GS (GYS) is a tetramer, which, like hemoglobin, can be described as a T or closed/inactive state. In a slight difference, one of the GS (GYS) subunits appears to adopt an asymmetric conformation, leading to close interactions with GN (GYG) and allowing the glycogen seed polymer on GN (GYG) to move to GS (GYS) for elongation (in a partially open state). Multiple conformations of the complex have been resolved. Further conformational changes lead to the open/active state, resulting in a more open binding groove for GN (GYG).
Figure \(\PageIndex{8}\) shows an interactive iCn3D model of the Human glycogenin-1 and glycogen synthase-1 complex in the presence of glucose-6-phosphate (8CVX). Glucose-6-phosphate is an allosteric activator of glycogen synthase.
Figure \(\PageIndex{8}\): Human glycogenin-1 and glycogen synthase-1 complex in the presence of glucose-6-phosphate (8CVX). (Copyright; author via source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...ivh4gZCupGcXZ7
The larger glycogen synthase subunits in the tetramer are shown in various colors, while the glycogenin fragments bound to each GS (GYS) monomer are shown in gray.
Figure \(\PageIndex{9}\) illustrates the conformational changes induced on the binding of glucose-6-phosphate to glycogen synthase.
Figure \(\PageIndex{9}\): G6P binding induces a conformational change across the GYS1 tetramer, leading to an open conformation for all four active sites. Fastman et a.l, ibid.
Panel (A) shows a cartoon representation of the +G6P GYS1:GYG1 complex (left) with GYS1 and GYG1 chains colored as in the previous figure. G6P is shown as spheres colored by heteroatom. Blue and yellow lines and boxes (right) indicate relative positions for perpendicular views. A black dotted circle indicates the oligomeric interface between the CTD-loop region and tetramerization core domains. The CTD loop, residues 484–488, forms cross-protomer interactions on the opposite side of the active site. Green dashed semicircles indicate open active sites.
Panel (B) shows interactions at the G6P-binding site. G6P (white) and proximal interacting residues are shown as sticks and colored by heteroatom. Yellow dotted lines indicate polar interactions.
Panel (C) shows changes at the G6P-binding site across conformations. A G6P-bound protomer is highlighted in orange, with G6P shown as spheres. The adjacent active state protomer (chain C) is shown in green cartoon. A basal state protomer (chain C) is modeled relative to the orange G6P-bound protomer and shown in yellow. Key changes to the G6P-sensing loop and a regulatory helix are highlighted by outline and non-transparent representation with arrows indicating the relevant motions. The rest of each chain is shown in a transparent cartoon representation.
We will return to the mechanism after exploring the last enzyme in the pathway.
Glycogen Branching Enzyme
The final enzyme, the glycogen branching enzyme (GBE), catalyzes the hydrolytic cleavage of an α(1→4) glycosidic linkage and subsequent inter- or intra-chain transfer of the non-reducing terminal fragment to the C6 hydroxyl position of an α-glucan (Figure \(\PageIndex{10}\)). In this example, an inter-chain transfer is occurring. At the top of the scheme, above the arrow, you can see that the GBE enzyme transiently removes several glucose residues (usually around 7) from one linear glycogen chain and then attaches it as an α1→6 branch to the other chain. In this process, an additional non-reducing end is created, which can act as a primer site for Glycogen Phosphorylase (the main enzyme that breaks down glycogen). Thus, glucose residues can be released very quickly when needed.
Details of the structure and domain organization of the human glycogen branching enzyme are shown in Figure \(\PageIndex{11}\). The four domains include N1, CBM48, the catalytic domain, and the C-terminal domain.
Figure \(\PageIndex{11}\): Crystal structure of hGBE1. Froese et al. Human Molecular Genetics, Volume 24, Issue 20, 15 October 2015, Pages 5667–5676, https://doi.org/10.1093/hmg/ddv280. Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/)
Panels (A and B) show orthogonal (perpendicular) views of hGBE1 showing the N-terminal helical segment (orange), CBM48 (pink), central catalytic domain (green), and C-terminal domain (blue). The catalytic triad Asp357-Glu412-Asp481 is shown as red sticks. Numbers refer to domain boundaries. N- and C-termini are labeled as grey spheres.
Panel (C) shows the superposition of branching enzyme structures from human (hGBE1, this study), O. sativa SBE1, and M. tuberculosis GBE, highlighting the conserved domain architecture and three regions of structural variation.
Panel (D) shows the domain organization of hGBE1, O. sativa SBE1, and M. tuberculosis GBE, revealing differences in the N-terminus between prokaryotic and eukaryotic polypeptides. Prokaryotic GBEs contain two N-terminal carbohydrate-binding domains (N1, N2,) whereas eukaryotes contain only one (CBM48) and replace the prokaryotic N1 domain with a helical extension.
Figure \(\PageIndex{12}\) shows an interactive iCn3D model of the human glycogen branching enzyme (GBE1)
Figure \(\PageIndex{12}\): human glycogen branching enzyme (GBE1). (Copyright; author via source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...47aqw5qto8hkU7
The domains in the iCn3D module are colored similarly to the previous figures.
The enzyme core is similar to that of amylase, with a conserved active site. Diseases of glycogen storage often result from mutations in the amylase core domain. For example, late-onset adult polyglucosan body disease (APBD) arises from a common mutation, Y329S. The effect of this mutation may be due to misfolding. A tetrapeptide, Leu-Thr-Lys-Glu, administered to patients, increased activity twofold, likely by acting as a chaperone to facilitate proper protein folding.
Putting it all together: Glycogen Synthesis and its Regulation
Figure \(\PageIndex{13}\) shows the steps involved in the addition of glucose from the donor UDP-glucose to glycogenin and through glycogen synthase to the growing glycogen polymer, which becomes branched through the activity of the glycogen branching enzyme.
Figure \(\PageIndex{13}\): Summary of glycogen synthesis. Marr, L., Biswas, D., Daly, L.A. et al. Nat Commun 13, 3372 (2022). https://doi.org/10.1038/s41467-022-31109-6. Creative Commons Attribution 4.0 International License. http://creativecommons.org/licenses/by/4.0/
The top reaction shows the step catalyzed by glycogenin (GN), while the bottom reactions are those catalyzed by glycogen synthase and the glycogen branching enzyme.
Glycogen synthesis is regulated in part by phosphorylation of key residues in both GS (GYS) and GN (GYG). Those sites are shown in Figure \(\PageIndex{14}\).
Figure \(\PageIndex{14}\): Domain and phosphorylation sites for glycogen synthase 1 (GS1) and glycogenin 1 (GN1). Marr et al., ibid.
Panel c shows the domain architecture of human GS (top) and GN (bottom). Known in vivo phosphorylation sites of GS are shown in red and labeled with the corresponding residue number and classical nomenclature (in bold). GN tyrosine 195, which becomes auto-glucosylated and was mutated to phenylalanine (Y195F) in this study, is indicated. Not to scale. Panel e shows the cartoon representation of GN WT and Y195F.
As we showed above, glycogen synthase is allosterically activated by glucose-6-phosphate binding, which can be thought to activate the enzyme via a T-to-R state change. The enzyme is inactivated by phosphorylation at multiple sites, as shown above. Activation can also occur through dephosphorylation. Phosphorylation of a site can create a binding site that facilitates additional phosphorylations. This can lead to a flexible "spike" of hyperphosphorylated residues forming from two monomers. Particularly important is pSer641 (site 3A), which interacts with a series of arginine residues in a regulatory helix of glycogen synthase. This arginine cluster has been referred to as the arginine cradle. The interaction sites are illustrated in Figure \(\PageIndex{15}\).
Figure \(\PageIndex{15}\): The phosphoregulatory region of human GS. Marr et al, ibid
Panel a shows the human (Hs)GS-GN34 structure in ribbons (top left). The N- and C-terminal tails of one GS protomer (chain A) lie next to one another and move towards the adjacent protomer, meeting the N- and C-terminal tails from chain B. Arrows indicate a continuation of cryo-EM density (top right). Electron density (C1 symmetry) for phosphorylated S641 (pS641) interacting with R588 and R591 on the regulatory helices α22 (bottom left). Residues interacting with the N- and C-terminal tails that are mutated in this study are shown (bottom right).
Panel b shows a comparison of distances between regulatory helices of adjacent monomers of HsGS (reported here), low activity inhibited mimic (PDB ID 5SUL), basal state (PDB ID 3NAZ), and G6P-activated (PDB ID 5SUK) yeast GS (yGS) crystal structures. Quoted distances were measured from Cα of Arg591 (chain A) and -Cα of Arg580 (chain B) of HsGS and corresponding yeast residues.
The strong electrostatic arginine-pSer interactions lock the tetramer into the inactive T state.
A cartoon model illustrating the regulation of glycogen synthase by phosphorylation/dephosphorylation and interconversion between T and R state is shown in Figure \(\PageIndex{16}\).
Figure \(\PageIndex{16}\): GS and GN cooperate to synthesize glycogen. Marr et al., ibid
The inhibition by phosphorylation can be relieved by binding the allosteric effector glucose-6-phosphate and does not require phosphatases.
Summary
(Summary written by Claude, Sonnet 4.6, Anthropic)
This chapter describes the enzymatic pathway of glycogen synthesis (glycogenesis) in mechanistic and structural detail, with particular attention to the regulation of glycogen synthase as the central controlled step in the pathway.
Glycogenesis requires six enzymes acting in sequence. Hexokinase phosphorylates glucose at C6 to produce glucose-6-phosphate, which phosphoglucomutase isomerizes to glucose-1-phosphate — positioning the anomeric carbon for activation. UDP-glucose pyrophosphorylase (UGPase) then catalyzes the nucleotidyl transfer of UMP from UTP to glucose-1-phosphate, forming UDP-glucose and releasing pyrophosphate. This reaction follows a sequential bi-bi mechanism in which UTP binds first in an Mg²⁺-coordinated active site, followed by glucose-1-phosphate; the metal ion organizes both substrates for nucleophilic attack of the phosphoryl oxygen of glucose-1-phosphate on the α-phosphorus of UTP. Pyrophosphate release is thermodynamically favorable and drives the reaction forward. UDP-glucose serves as the universal activated glucosyl donor throughout glycan biosynthesis — for glycogen, starch, cellulose, glycoproteins, and glycolipids — reflecting the metabolic centrality of this intermediate. Human UGPase is a tetrameric (and in some forms octameric) enzyme whose activity is sensitive to structural perturbations in the latch loop (particularly Glu412) and the SB and 309 loops at subunit interfaces, as revealed by mutagenesis studies showing that steric effects at inter-subunit contacts are more important than charge alone.
Glycogen synthesis cannot begin de novo with glycogen synthase alone, as the enzyme requires a pre-existing primer of 4–6 α1→4-linked glucose residues. This primer is provided by glycogenin, a dimeric self-glucosylating protein that attaches the first glucose residue via a transglycosylation reaction to its own Tyr-194 hydroxyl group, using UDP-glucose coordinated by Mn²⁺ and conserved aspartate residues. Glycogenin then extends this primer by up to approximately 8 residues before handing it off to glycogen synthase.
Recent cryo-EM structures of the human glycogenin-1/glycogen synthase-1 complex reveal that the two enzymes operate in intimate physical association, cycling through at least three conformational states: a closed/inactive state in which the glycogen synthase tetramer adopts a T-like conformation, a partially open state in which an asymmetric GS subunit contacts glycogenin and positions the primer for transfer, and an open/active state with a widened binding groove for glycogenin. Glucose-6-phosphate binding to glycogen synthase drives the transition to the active state by repositioning the G6P-sensing loop and a regulatory helix, opening all four active sites simultaneously through allosteric communication across the tetramer interface — a structural mechanism analogous to the T-to-R transition in hemoglobin.
Once the primer is transferred, glycogen synthase extends the main chain by iteratively transferring the glucosyl unit from UDP-glucose to the C4-OH of the non-reducing terminal residue, forming new α1→4 linkages with UDP as the leaving group. Chain elongation continues until a segment of approximately 11 residues is available for branching. The glycogen branching enzyme (GBE1) then cleaves an α1→4 linkage approximately 7 residues from the non-reducing end and transfers the oligosaccharide fragment to a C6-OH of the same or another chain, forming an α1→6 branch point. This reaction is mechanistically analogous to amylase, sharing a conserved Asp-Glu-Asp catalytic triad and core domain architecture. Branching is essential because it creates additional non-reducing ends — the sites of both elongation and phosphorolytic degradation — dramatically increasing the number of sites available for rapid glucose mobilization.
Glycogen synthase activity is regulated at multiple levels. Allosteric activation by glucose-6-phosphate stabilizes the active R state and can override the inhibitory effects of phosphorylation without requiring phosphatase action. Covalent regulation involves phosphorylation at multiple serine residues by several kinases including GSK-3; phosphorylation at one site can create a recognition sequence for a subsequent kinase, leading to hierarchical hyperphosphorylation of an N- and C-terminal "spike" emanating from the tetramer. Critical to the inactive T state is the interaction of phosphoserine-641 (pSer641) at site 3A with the arginine cradle — a cluster of arginine residues on the regulatory helix α22 of the adjacent subunit — which electrostatically locks the tetramer in a closed, inactive conformation. Dephosphorylation by PP1, activated downstream of insulin signaling via Akt-mediated inactivation of GSK-3, reverses this inhibition and restores the active state. The integration of allosteric and covalent regulation ensures that glycogen synthesis is precisely coupled to cellular energy status — activated when glucose-6-phosphate is abundant, and insulin signaling is high, and suppressed when glucose is scarce, and when catabolic hormones such as glucagon activate PKA-mediated phosphorylation cascades.
References
1. Kumpf, A., Partzsch, A., Pollender, A., Bento, I., and Tischler, D. (2019) Two Homologous Enzymes of the GalU Family in Rhodococcus opacus 1CP-RoGalU1 and RoGalU2. Int. J. Mol. Sci. 20(22), 5809. https://doi.org/10.3390/ijms20225809




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