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

GCNT2



General Information
Gene Symbol:   
GCNT2
Protein name:   
N-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase
Enzyme Class:   
Glycosyltransferase
CAZy Family:   
E.C. No:   
Organs:   
Reaction (SNFG):   
+
+ UDP
Reaction (IUBMB):   
No specified reaction.

About

• This is the β1,6-N-acetylglucosaminyltransferase or IGnT enzyme, forming the GlcNAcβ1-3(GlcNAcβ1-6)Galβ1-3GalNAcα1-R branch from the linear GlcNAcβ1-3Galβ1-3GalNAcα1-R lactosamine structure.
• In humans, GCNT2 is expressed as three spliced variants IGnTA, IGnTB and IGnTC.
• GCNT2 is overexpressed in highly metastatic breast cancer cell lines and basal-like breast tumor samples. Thus, GCNT2 expression correlates with metastatic phenotype of tumors.
• GCNT2 also enhances cell detachment, adhesion to endothelial cells, cell migration and invasion in vitro, and lung metastasis of breast cancer cells in vivo.


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:  
     N-linked, O-linked (mucin type), GSL
Compartment:  
     Cis, Medial, Trans, TGN
Substrate:  
     Gal(b1-4)GlcNAc(b1-3)Gal(b1-4)GlcNAc(b1-?)
Product:  
     Gal(b1-4)GlcNAc(b1-3)[GlcNAc(b1-6)]Gal(b1-4)GlcNAc(b1-?)

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 8 6 4 2 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 60 50 40 30 20 10 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
ENST00000265012 ENST00000316170 ENST00000379597 ENST00000397423 ENST00000410107 ENST00000474983 ENST00000489225 ENST00000489819 OTX2 TAF1 SMAD4 NANOG OTX2 YY1 SOX2 TAL1 FOXA1 TBP SP1 TEAD4 NANOG ZNF449


miRNA-GlycoEnzyme Interactome {ref. 9}
GCNT2/hsa-miR-216a-3p
miRNA Target Site Type Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
5'...AAAUAUCCACUGGA CACUGUGA ...
3'   UAUUAGGGUCUCUG GUGACAC U
8mer 158-165 -0.299 97.0 -0.299 98.0 con
5'...ACCUUAACAGUCAC CACUGUG C...
3'   UAUUAGGGUCUCUG GUGACAC U
7mer-m8 423-429 -0.061 68.0 -0.061 77.0 noncon