FuncClass

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

B4GALNT4



General Information
Gene Symbol:   
B4GALNT4
Protein name:   
N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase 1
Enzyme Class:   
Glycosyltransferase
CAZy Family:   
GT7
E.C. No:   
Organs:   
Reaction (SNFG):   
+
+ UDP
Reaction (IUBMB):   
No specified reaction.

About

• The nonreducing terminal GalNAc(β1-4)GlcNAc (LacdiNAc or LDN) group is found as part of N- and O-linked glycans of both vertebrate and invertebrate glycoproteins (PMID: 25003135). This structure is synthesized by two enzymes B4GALNT3 and B4GALNT4.
• LacdiNAc structures are less abundant compared to Type-II lactosamine chains and they have been reported on a limited number of proteins including pituitary prolactin, lutropin (LH), follitropin (FSH), glycodelin and Tissue Factor Pathway Inhibitors (TFPI). They are also formed in epithelial cells of kidney and breast origin.
• Enzyme activity may be peptide core specific suggesting biological importance of such modifications. Due to this peptide specificity the distribution of this substructure may also be limited.
• The β1,4-linked GalNAc can be further modified with a variety of moieties: 4-linked SO4, α2,6-Neu5Ac, or at the subterminal by α1,3-fuc. This results in additional epitopes like 4SGalNAc(β1-4)GlcNAcβ, Siaα(2-6)GalNAc(β1-4)GlcNAcβ, GalNAc(β1-4)[Fuc(α1-3)]GlcNAcβ etc.
• β4GalNAc-T3 and β4GalNAc-T4 transcripts are widely expressed. β4GalNAc-T3 transcript is most abundant in the stomach, colon, and testis. β4GalNAc-T4 transcript is abundant in the ovary, brain, colon, uterus, fetal brain, kidney, and lung.
• Wisteria floribunda agglutinin binds β-linked GalNAc, and is used to monitor B4GalNT3,4 activity in tissue sections.
• β4GalNAc-T3 is upregulated in 75 % of primary colon cancers, correlating with a more malignant phenotype. Enzyme activity related to LacdiNAc is also dysregulated during other cancers: ovarian, pancreatic, prostate and breast.


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)
Compartment:  
     
Substrate:  
     GlcNAc(b1-?)
Product:  
     GalNAc(b1-4)GlcNAc(b1-?)

Simulation Parameters
Mechaelis-Menten parameters (suggested)
VM:    3.70e-06    (pmol/cell • hr)       KM:    7.00e+08    (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 10 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 50 40 30 20 10 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-3144-5p 199-206 -0.56 99.0 -0.56 99.0 noncon
hsa-miR-4749-3p 98-105 -0.525 99.0 -0.525 99.0 noncon
hsa-miR-3615 73-80 -0.406 94.0 -0.406 96.0 noncon
hsa-miR-3120-3p 231-238 -0.379 99.0 -0.379 99.0 noncon
hsa-miR-4427 289-296 -0.356 99.0 -0.322 99.0 noncon
hsa-miR-4726-5p 132-139 -0.326 94.0 -0.326 95.0 noncon
hsa-miR-4640-5p 132-139 -0.324 94.0 -0.324 95.0 noncon
hsa-miR-1324 272-278 -0.28 97.0 -0.254 97.0 noncon
hsa-miR-3937 112-118 -0.274 92.0 -0.274 95.0 noncon
hsa-miR-22-3p 39-45 -0.261 92.0 -0.261 94.0 noncon
hsa-miR-548v 234-240 -0.25 91.0 -0.25 94.0 noncon