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

B4GALNT3



General Information
Gene Symbol:   
B4GALNT3
Protein name:   
Beta-1,4-N-acetylgalactosaminyltransferase 3
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:  
     Cis, Medial, Trans, TGN
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 40 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 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-877-3p 1036-1043 -0.468 98.0 -0.468 99.0 noncon
hsa-miR-7108-3p 1091-1098 -0.407 95.0 -0.407 96.0 noncon
hsa-miR-7847-3p 1925-1932 -0.381 97.0 -0.381 98.0 noncon
hsa-miR-6887-3p 2015-2022 -0.366 95.0 -0.366 96.0 noncon
hsa-miR-877-3p 863-869 -0.343 97.0 -0.343 97.0 noncon
hsa-miR-4999-5p 2031-2038 -0.325 95.0 -0.325 97.0 noncon
hsa-miR-6801-3p 797-804 -0.306 94.0 -0.306 96.0 noncon
hsa-miR-4665-5p 339-346 -0.298 93.0 -0.298 95.0 noncon
hsa-miR-6826-3p 2016-2023 -0.298 94.0 -0.298 95.0 noncon
hsa-miR-541-3p 1829-1835 -0.296 95.0 -0.296 96.0 noncon
hsa-miR-4758-3p 1722-1729 -0.293 95.0 -0.293 96.0 noncon
hsa-miR-365a-3p 639-646 -0.289 95.0 -0.289 96.0 con
hsa-miR-365b-3p 639-646 -0.289 95.0 -0.289 96.0 con
hsa-miR-296-5p 16-23 -0.288 90.0 -0.288 92.0 noncon
hsa-miR-3612 1318-1325 -0.285 96.0 -0.285 97.0 noncon
hsa-miR-1306-5p 1111-1118 -0.279 95.0 -0.279 97.0 noncon
hsa-miR-650 1318-1325 -0.277 96.0 -0.277 97.0 noncon
hsa-miR-4258 1092-1098 -0.275 91.0 -0.275 93.0 noncon
hsa-miR-3943 919-925 -0.266 93.0 -0.266 95.0 noncon
hsa-miR-323a-5p 368-375 -0.265 94.0 -0.265 95.0 noncon
hsa-miR-6810-3p 797-804 -0.264 92.0 -0.264 94.0 noncon
hsa-miR-654-5p 1829-1835 -0.263 93.0 -0.263 95.0 noncon
hsa-miR-1306-5p 1390-1397 -0.262 94.0 -0.262 96.0 noncon
hsa-miR-1260a 2011-2017 -0.25 92.0 -0.25 94.0 noncon
hsa-miR-1260b 2011-2017 -0.25 92.0 -0.25 94.0 noncon