Comprehensive glycoEnzyme database and dynamic pathway generation

Description: The GlycoEnzDB is a manually curated glycoEnzyme database, primarily focused on humans. It covers 390 enzymes across 28 pathway maps. Facilities are also available to create custom glycosylation reaction pathways using experimental data in SBML format and for pathway simulation
Contacts: Sriram Neelamegham (, Yusen Zhou ( or Ted Groth (

Create glycosylation pathway
Custom database generation

Pathway Map


General Information
Gene Symbol:   
Protein name:   
Exostosin-like 3
Enzyme Class:   
CAZy Family:   
E.C. No:   
Reaction (SNFG):   
Reaction (IUBMB):   
No specified reaction.


• The initiation of heparan sulfate biosynthesis is catalyzed by an αGlcNAc transferase activity that is termed ?GlcNAcT-I?. Addition of GlcA (HS-GlcAT-II) and GlcNAc (GlcNAcT-II) then ensues to form an HS backbone.
• These activities are mediated by several enzymes of the EXT (EXT-1/2) and EXT-like (EXTL-1/2/3) gene family. EXTL-1, -2 and -3 all have only HexNAc transferase activity, and they were discovered after EXT1/2. EXT1/2 have dual enzyme activity.
• EXTL3 has both GlcNAcT-I activity and GlcNAcT-II activity. Thus, it participate in both chain initiation and extension. EXTL3 knockout is embryonic lethal, it is most likely responsible for adding the first GlcNAc to the tetrasaccharide linker to initiate HS chain extension by EXT1/EXT2. Homozygous mutation of EXTL3 has recently been found to cause severe developmental delay.
• EXTL2 (α1,4-N-Acetylhexosaminyltransferase) catalyzes the transfer of a α(1-4)GlcNAc or alternatively α(1-4)GalNAc residue from UDP-GalNAc/GlcNAc to the core oligosaccharide representing the GAG-protein linker (i.e. GlcNAcT-I activity). EXTL2 is widely distributed in various mammalian tissues and cells as well as in serum. α-GalNAc activity of EXTL2 may suppress HS biosynthesis, as this can no longer be extended by EXT1/EXT2. EXTL2 knockout mice is largely normal but shown various defects when challenged with disease models.
• EXTL1 only has GlcNAcT-II activity.
• EXT1 and EXT2 form a heterodimeric complex of Type II-proteins in cis-Golgi. EXT1-EXT2 interaction and core proteins are critical and required for the heparan chain polymerization reactions.
• EXT1 (Exostosin) and EXT2 both have GlcAT and GlcNAcT activities (i.e. they are bifunctional) and are together responsible for HS chain polymerization. Knocking out either EXT1 or EXT2 is embryonic lethal.
• Even heterozygous mutations in EXT1 or EXT2 led to reduction in HS biosynthesis and can cause a bone disease called Exostosis.

Related Pathway
KEGG Pathway:   

Related Database
Homo sapiens
NCBI GeneID:   
GlyMap GeneID:   
DNA aRefSeq:   
Protein RefSeq:   
OMIM number:   
GeneCards database:   

Enzyme Specificity
Glycan Type:  
     ER, Cis, Medial, Trans, TGN

Simulation Parameters
Mechaelis-Menten parameters (suggested)
VM:       (pmol/cell • hr)       KM:       (pM)
Relative conc of enzymes in compartment.(sum will be normalized to 1)
ER Cis- Medial- Trans- TGN

Expression Data in Tissue {ref. 5} Source from NCBI gene database
adrenal appendix bone marrow brain colon duodenum endometrium esophagus fat gall bladder heart kidney liver lung lymph node ovary pancreas placenta prostate salivary gland skin small intestine spleen stomach testis thyroid urinary bladder 20 10 0 RPKM
Expression Data in Cells {ref. 13} Source from Cancer Cell Line Encyclopedia database
Kidney Lung Breast Prostate Large intestine Ovary HL60 haematopoietic and lymphoid tissue Skin Central nervous system 786O A498 ACHN CAKI1 UO31 A549 EKVX HOP62 HOP92 NCIH226 NCIH23 NCIH322 NCIH460 NCIH522 SHP77 BT549 HS578T MCF7 MDAMB231 MDAMB468 T47D DU145 PC3 HCT116 HCT15 HT29 KM12 SW620 OVCAR4 OVCAR8 IGROV1 SKOV3 HL60 K562 RPMI8226 LOXIMVI MALME3M RPMI7951 SKMEL28 SKMEL5 UACC257 UACC62 SF268 SF295 SF539 SNB75 100 80 60 40 20 0 Transcripts per million (TPM)
Transcription factor {ref. 10}
No high degree of confidence data

miRNA-GlycoEnzyme Interactome {ref. 9}
miRNA Name Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
hsa-miR-6749-3p 36-43 -0.45 98.0 -0.45 98.0 noncon
hsa-miR-3622b-5p 2721-2728 -0.409 98.0 -0.405 99.0 noncon
hsa-miR-92b-5p 2541-2548 -0.407 92.0 -0.403 94.0 noncon
hsa-miR-361-3p 441-448 -0.382 98.0 -0.378 98.0 noncon
hsa-miR-136-5p 2803-2810 -0.38 98.0 -0.376 98.0 con
hsa-miR-585-3p 284-291 -0.372 96.0 -0.372 97.0 noncon
hsa-miR-3135a 60-67 -0.35 94.0 -0.35 96.0 noncon
hsa-miR-608 2736-2743 -0.332 90.0 -0.329 92.0 noncon
hsa-miR-6827-5p 47-54 -0.328 93.0 -0.328 95.0 noncon
hsa-miR-652-3p 571-577 -0.306 90.0 -0.303 94.0 noncon
hsa-miR-4424 2813-2820 -0.302 96.0 -0.004 23.0 noncon
hsa-miR-939-3p 287-294 -0.291 96.0 -0.291 97.0 noncon
hsa-miR-5196-3p 23-30 -0.275 96.0 -0.275 97.0 noncon
hsa-miR-2355-5p 15-22 -0.251 95.0 -0.251 96.0 noncon