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MetaCyc Pathway: heparan sulfate biosynthesis (late stages)
Traceable author statement to experimental support

Pathway diagram: heparan sulfate biosynthesis (late stages)

Note: a dashed line (without arrowheads) between two compound names is meant to imply that the two names are just different instantiations of the same compound -- i.e. one may be a specific name and the other a general name, or they may both represent the same compound in different stages of a polymerization-type pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: BiosynthesisCarbohydrates BiosynthesisPolysaccharides BiosynthesisGlycosaminoglycans Biosynthesis

Some taxa known to possess this pathway include : Homo sapiens

Expected Taxonomic Range: Metazoa


Heparan sulfate is a linear polysaccharide found in all animal tissues. It occurs as a proteoglycan in which two or three heparan sulfate chains are attached to cell surface or extracellular matrix proteins, known as "core proteins". Heparan sulfate binds to diverse protein ligands (known as heparin-binding proteins) and regulates a wide variety of biological activities, including developmental processes, cell adhesion and motility, angiogenesis, blood coagulation and tumour metastasis.

The molecule is built of glycosaminoglycan chains attached to specific serine residues in a core protein. The chains are composed of a simple sugar backbone that is modified to different degrees depending on the cellular conditions. The backbone is built of several types of disaccharide building units with different sulfation patterns and can accomodate over 1,000,000 different sequences built up of up to 200 disaccharide units [Sasisekharan00].

The disaccharide building units are composed of a hexose sugar and a uronic acid. The most common repeating unit, which makes up around 50% of the total disaccharide units in heparan sulfate, is composed of β-D-glucuronate linked to N-acetyl-α-D-glucosamine. In other units β-D-glucuronate may be substituted by α-L-iduronate or its sulfated form α-L-iduronate 2-O-sulfate, and N-acetyl-β-D-glucosamine may be sulfated to N-sulfo-D-glucosamine, α-D-N-sulfoglucosamine 6-O-sulfate, a [heparan sulfate]-α-D-N-sulfoglucosamine 3-O-sulfate or a [heparan sulfate]-α-D-N-sulfoglucosamine 3,6-O-bissulfate.

Heparan sulfate chains comprise three different types of domains: S-domains that contain contiguous N-sulfated residues, unmodified N-acetyl-rich regions, and mixed transition zones between the S-domains and the unmodified segments. Only the S-domains have binding capacities for growth factors and other proteins [Gallagher01]. The structure of heparin is very similar, but its chains are not organized into distinct sulfated and non-sulfated domains [Murphy04].

The synthesis of heparan sulfate takes place in the Golgi apparatus, with the exception of the first reaction, the attachemnt of xylose to the core protein, which takes place within the endoplasmic reticulum.

About This Pathway

The synthesis of heparan sulfate begins with the formation of a tetrasaccharide linkage region on the core protein, as described in glycoaminoglycan-protein linkage region biosynthesis. Once the linkage region is synthesized, a key reaction, catalyzed by EXTL2 and EXTL3, adds an N-acetyl-α-D-glucosamine residue to the linkage region tetrasaccharide. This addition is a molecular switch that prevents the synthesis of chondroitin sulfate or dermatan sulfate on the linkage region. The chain is then elongated by the exostosin complex, a bifunctional protein composed of EXT1 and EXT2 units, that can add both β-D-glucuronate and N-acetyl-α-D-glucosamine in an alternating manner to the nascent chain. Once the basic backbone is synthesized, many enzymes alter the structure.

A key enzyme is the bifunctional heparan sulfate N-deacetylase/N-sulfotransferase (4 isoforms are encoded by NDST1, NDST2, NDST3 and NDST4). The enzyme removes the acetyl groups from a [heparan]-N-acetyl-α-D-glucosamine residues in what would become S-regions, and sulfates the free NH2 groups, resulting in a [heparan sulfate]-α-D-N-sulfoglucosamine.

Heparosan-N-sulfate-glucuronate 5-epimerase ( GLCE) converts β-D-glucuronate residues to α-L-iduronate residues. [Heparan sulfate]-uronosyl-2-O-sulfotransferase 1 ( HS2ST1), which interacts with GLCE, transfers a sulfate group to the C2 position of the α-L-iduronate residues.

Finally, a set of 3-O-sulfotransferases and 6-O-sulfotransferases act on the a [heparan sulfate]-α-D-N-sulfoglucosamine residues, resulting in formation of the bi-sulfated forms a [heparan sulfate]-α-D-N-sulfoglucosamine 3-O-sulfate, a [heparan sulfate]-α-D-N-sulfoglucosamine 6-O-sulfate and the triple-sulfated a [heparan sulfate]-α-D-N-sulfoglucosamine 3,6-O-bissulfate residues.

Superpathways: heparan sulfate biosynthesis

Created 04-Aug-2010 by Caspi R, SRI International


Casu89: Casu, B. (1989). "in Heparin: Chemical and Biological Properties, Clinical Applications." Lane, D. A., and Lindahl, U., Eds, pp 25-49, CRC Press, Boca Raton, FL.

Gallagher01: Gallagher JT (2001). "Heparan sulfate: growth control with a restricted sequence menu." J Clin Invest 108(3);357-61. PMID: 11489926

Gatti79: Gatti, G., Casu, B., Hamer, G. K., Pelin, A. S. (1979). Macromolecules 12:1001-1007.

Hovingh70: Hovingh P, Linker A (1970). "The enzymatic degradation of heparin and heparitin sulfate. 3. Purification of a heparitinase and a heparinase from flavobacteria." J Biol Chem 245(22);6170-5. PMID: 5484472

Murphy04: Murphy KJ, Merry CL, Lyon M, Thompson JE, Roberts IS, Gallagher JT (2004). "A new model for the domain structure of heparan sulfate based on the novel specificity of K5 lyase." J Biol Chem 279(26);27239-45. PMID: 15047699

Rosenberg97: Rosenberg RD, Shworak NW, Liu J, Schwartz JJ, Zhang L (1997). "Heparan sulfate proteoglycans of the cardiovascular system. Specific structures emerge but how is synthesis regulated?." J Clin Invest 99(9);2062-70. PMID: 9151776

Sasisekharan00: Sasisekharan R, Venkataraman G (2000). "Heparin and heparan sulfate: biosynthesis, structure and function." Curr Opin Chem Biol 4(6);626-31. PMID: 11102866

Sugahara02: Sugahara K, Kitagawa H (2002). "Heparin and heparan sulfate biosynthesis." IUBMB Life 54(4);163-75. PMID: 12512855

Trowbridge02: Trowbridge JM, Gallo RL (2002). "Dermatan sulfate: new functions from an old glycosaminoglycan." Glycobiology 12(9);117R-25R. PMID: 12213784

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Ahn95: Ahn J, Ludecke HJ, Lindow S, Horton WA, Lee B, Wagner MJ, Horsthemke B, Wells DE (1995). "Cloning of the putative tumour suppressor gene for hereditary multiple exostoses (EXT1)." Nat Genet 11(2);137-43. PMID: 7550340

Aikawa01: Aikawa J, Grobe K, Tsujimoto M, Esko JD (2001). "Multiple isozymes of heparan sulfate/heparin GlcNAc N-deacetylase/GlcN N-sulfotransferase. Structure and activity of the fourth member, NDST4." J Biol Chem 276(8);5876-82. PMID: 11087757

Aikawa99: Aikawa J, Esko JD (1999). "Molecular cloning and expression of a third member of the heparan sulfate/heparin GlcNAc N-deacetylase/ N-sulfotransferase family." J Biol Chem 274(5);2690-5. PMID: 9915799

Campbell94: Campbell P, Hannesson HH, Sandback D, Roden L, Lindahl U, Li JP (1994). "Biosynthesis of heparin/heparan sulfate. Purification of the D-glucuronyl C-5 epimerase from bovine liver." J Biol Chem 269(43);26953-8. PMID: 7929434

Crawford01: Crawford BE, Olson SK, Esko JD, Pinhal MA (2001). "Cloning, Golgi localization, and enzyme activity of the full-length heparin/heparan sulfate-glucuronic acid C5-epimerase." J Biol Chem 276(24);21538-43. PMID: 11279150

Dixon95: Dixon J, Loftus SK, Gladwin AJ, Scambler PJ, Wasmuth JJ, Dixon MJ (1995). "Cloning of the human heparan sulfate-N-deacetylase/N-sulfotransferase gene from the Treacher Collins syndrome candidate region at 5q32-q33.1." Genomics 26(2);239-44. PMID: 7601448

Duncan01: Duncan G, McCormick C, Tufaro F (2001). "The link between heparan sulfate and hereditary bone disease: finding a function for the EXT family of putative tumor suppressor proteins." J Clin Invest 108(4);511-6. PMID: 11518722

Duncan06: Duncan MB, Liu M, Fox C, Liu J (2006). "Characterization of the N-deacetylase domain from the heparan sulfate N-deacetylase/N-sulfotransferase 2." Biochem Biophys Res Commun 339(4);1232-7. PMID: 16343444

Grobe02: Grobe K, Esko JD (2002). "Regulated translation of heparan sulfate N-acetylglucosamine N-deacetylase/n-sulfotransferase isozymes by structured 5'-untranslated regions and internal ribosome entry sites." J Biol Chem 277(34);30699-706. PMID: 12070138

Habuchi00: Habuchi H, Tanaka M, Habuchi O, Yoshida K, Suzuki H, Ban K, Kimata K (2000). "The occurrence of three isoforms of heparan sulfate 6-O-sulfotransferase having different specificities for hexuronic acid adjacent to the targeted N-sulfoglucosamine." J Biol Chem 275(4);2859-68. PMID: 10644753

Habuchi03: Habuchi H, Miyake G, Nogami K, Kuroiwa A, Matsuda Y, Kusche-Gullberg M, Habuchi O, Tanaka M, Kimata K (2003). "Biosynthesis of heparan sulphate with diverse structures and functions: two alternatively spliced forms of human heparan sulphate 6-O-sulphotransferase-2 having different expression patterns and properties." Biochem J 371(Pt 1);131-42. PMID: 12492399

Habuchi95: Habuchi H, Habuchi O, Kimata K (1995). "Purification and characterization of heparan sulfate 6-sulfotransferase from the culture medium of Chinese hamster ovary cells." J Biol Chem 270(8);4172-9. PMID: 7876170

Habuchi98: Habuchi H, Kobayashi M, Kimata K (1998). "Molecular characterization and expression of heparan-sulfate 6-sulfotransferase. Complete cDNA cloning in human and partial cloning in Chinese hamster ovary cells." J Biol Chem 273(15);9208-13. PMID: 9535912

Hernaiz00: Hernaiz M, Liu J, Rosenberg RD, Linhardt RJ (2000). "Enzymatic modification of heparan sulfate on a biochip promotes its interaction with antithrombin III." Biochem Biophys Res Commun 276(1);292-7. PMID: 11006120

Humphries97: Humphries DE, Sullivan BM, Aleixo MD, Stow JL (1997). "Localization of human heparan glucosaminyl N-deacetylase/N-sulphotransferase to the trans-Golgi network." Biochem J 325 ( Pt 2);351-7. PMID: 9230113

Humphries98: Humphries DE, Lanciotti J, Karlinsky JB (1998). "cDNA cloning, genomic organization and chromosomal localization of human heparan glucosaminyl N-deacetylase/N-sulphotransferase-2." Biochem J 332 ( Pt 2);303-7. PMID: 9601056

Jacobsson84: Jacobsson I, Lindahl U, Jensen JW, Roden L, Prihar H, Feingold DS (1984). "Biosynthesis of heparin. Substrate specificity of heparosan N-sulfate D-glucuronosyl 5-epimerase." J Biol Chem 259(2);1056-63. PMID: 6420398

Jemth03: Jemth P, Smeds E, Do AT, Habuchi H, Kimata K, Lindahl U, Kusche-Gullberg M (2003). "Oligosaccharide library-based assessment of heparan sulfate 6-O-sulfotransferase substrate specificity." J Biol Chem 278(27);24371-6. PMID: 12702732

Kakuta99: Kakuta Y, Sueyoshi T, Negishi M, Pedersen LC (1999). "Crystal structure of the sulfotransferase domain of human heparan sulfate N-deacetylase/ N-sulfotransferase 1." J Biol Chem 274(16);10673-6. PMID: 10196134

Kim01: Kim BT, Kitagawa H, Tamura J, Saito T, Kusche-Gullberg M, Lindahl U, Sugahara K (2001). "Human tumor suppressor EXT gene family members EXTL1 and EXTL3 encode alpha 1,4- N-acetylglucosaminyltransferases that likely are involved in heparan sulfate/ heparin biosynthesis." Proc Natl Acad Sci U S A 98(13);7176-81. PMID: 11390981

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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