GlyClass

GlycoEnzDB
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 (neel@buffalo.edu), Yusen Zhou (yusenzho@buffalo.edu) or Ted Groth (tgroth@buffalo.edu).

GlycoEnzDB
Create glycosylation pathway
Custom database generation
Instructions/Reference
 

Pathway Map

GCNT1



General Information
Gene Symbol:   
GCNT1
Protein name:   
Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase
Enzyme Class:   
Glycosyltransferase
CAZy Family:   
E.C. No:   
Organs:   
Reaction (SNFG):   
+
+ UDP
Reaction (IUBMB):   
No specified reaction.

About

• This is C2GnT-1 or C2GnT-L (leukocyte type) or core-2 GlcNAcT that forms the core-2 branch on O-glycans. It is widely expressed in human leukocytes and also other tissue.
• Its level is low in naive T-cells but increases upon T-cell activation.
• C2GnT-I upregulation also promotes metastasis in colorectral, lung and prostate cancer.
• C2GnT-I is a major contributor to L- and P-selectin binding during inflammation.
• Addition of sulfotransferase activity can result in the formation of 6-sulfo sialyl Lex structures on these core-2 glycans that act as L-selectin ligands in the HEV.
• GCNT1 is over-expressed in some diseases Wiskott-Aldrich syndrome (WAS), leukemia and AIDS. This contributes to immunodeficient conditions due to abherent T-cell function.
• Core2 branch is a scaffold for the subsequent production of lactosamine disaccharide repeat, poly-N-acetyllactosamine (Galβ1-4GlcNAc)n which is a ligand for galectin-3.
• Core-2 branch in general adds bulk to the O-glyans and this may reduce other interactions like TRAIL binding to DR4-- thus it is immunomodulatory.


Related Pathway
KEGG ORTHOLOGY:   
KEGG Pathway:   
Reactome:   

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

Enzyme Specificity
Glycan Type:  
     O-linked (mucin type)
Compartment:  
     Cis, Medial, Trans, TGN
Substrate:  
     Gal(b1-3)GalNAc(a1-?)Ser|Thr
Product:  
     Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-?)Ser|Thr
Constraints:  
     !NeuAc(a2-3)Gal(b1-3)GalNAc(a1-?)&!Gal(b1-3 [3S])GalNAc(a1-?)

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 30 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}
Transcriptional start site (TSS) 0 200 -2000 -1800 -1600 -1400 -1200 -1000 -800 -600 -400 -200
ENST00000376730 ENST00000442371 ENST00000444201 ENST00000480311 TCF12 RUNX3 TSC22D4 MYB BATF3 ETV6 MTA2 SP1 CREM CREM IRF4 BATF RBPJ JUNB JUND FOS ELF3 MYC FOSL2 ARID3A


miRNA-GlycoEnzyme Interactome {ref. 9}
GCNT1/hsa-miR-301b-5p
miRNA Target Site Type Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
5'...UAGUAGAUCUUCUU GUCAGAGA ...
3'   UCAUCACGUUGGAG CAGUCUC G
8mer 132-139 -0.257 98.0 -0.257 98.0 noncon