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
B3GAT1



General Information
Gene Symbol:   
B3GAT1
Protein name:   
Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1
Enzyme Class:   
Glycosyltransferase
CAZy Family:   
GT43
E.C. No:   
2.4.1.135
Organs:   
Reaction (SNFG):   
+
→
+ UDP
Reaction (IUBMB):   
No specified reaction.
About

• Involved in the biosynthesis of the HNK-1 epitope.
• Can also play a role in glycosaminoglycan biosynthesis.

Related Pathway
KEGG ORTHOLOGY:   
K00735
KEGG Pathway:   
ko00515  ko01100 
Reactome:   
R-HSA-1971475
Related Database
Organism:   
Homo sapiens
Uniprot:   
Q9P2W7 
NCBI GeneID:   
27087
GlyMap GeneID:   
27087
DNA aRefSeq:   
NM_018644.3 
Protein RefSeq:   
NP_061114.2 
BRENDA:   
Kinetic info.
OMIM number:   
151290
GeneCards database:   
B3GAT1
Enzyme Specificity
Glycan Type:  
     N-linked, O-linked (mucin type), GSL
Compartment:  
     ER, Cis, Medial, Trans, TGN
Substrate:  
     Gal(b1-4)GlcNAc(b1-?)
Product:  
     GlcA(b1-3)Gal(b1-4)GlcNAc(b1-?)
Constraints:  
     !GlcA(b1-3)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 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}
Transcriptional start site (TSS) 0 200 -2000 -1800 -1600 -1400 -1200 -1000 -800 -600 -400 -200
ENST00000312527 ENST00000392580 ENST00000531778 GATA3 ZNF146 ASCL1 MAX RUNX1 SP1 TAL1 EGR3 EGR2 ETS1 ZFHX2 NCOR1 NCOR1 TCF3 MYC TCF12 IKZF1 FLI1
miRNA-GlycoEnzyme Interactome {ref. 9}
miRNA Name Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
hsa-miR-3169 2250-2257 -0.691 99.0 -0.635 99.0 noncon
hsa-miR-3117-3p 2251-2258 -0.614 99.0 0.0 8.0 noncon
hsa-miR-7109-5p 1393-1400 -0.448 97.0 -0.448 98.0 noncon
hsa-miR-6887-5p 1392-1399 -0.437 94.0 -0.437 95.0 noncon
hsa-miR-6795-5p 1392-1399 -0.437 94.0 -0.437 95.0 noncon
hsa-miR-5008-3p 175-182 -0.432 98.0 -0.432 99.0 noncon
hsa-miR-6737-3p 175-182 -0.419 98.0 -0.419 99.0 noncon
hsa-miR-7157-3p 175-182 -0.419 98.0 -0.419 99.0 noncon
hsa-miR-711 2041-2048 -0.405 98.0 -0.405 98.0 noncon
hsa-miR-7108-3p 364-371 -0.403 95.0 -0.403 96.0 noncon
hsa-miR-4713-3p 614-621 -0.402 95.0 -0.402 96.0 noncon
hsa-miR-4706 298-305 -0.394 95.0 -0.394 96.0 noncon
hsa-miR-128-1-5p 807-814 -0.394 98.0 -0.394 98.0 noncon
hsa-miR-1233-5p 1602-1609 -0.392 97.0 -0.392 98.0 noncon
hsa-miR-3162-5p 1191-1198 -0.391 97.0 -0.391 98.0 noncon
hsa-miR-6778-5p 1602-1609 -0.384 97.0 -0.384 98.0 noncon
hsa-miR-4749-5p 298-305 -0.352 92.0 -0.352 94.0 noncon
hsa-miR-541-3p 1219-1225 -0.351 97.0 -0.351 97.0 noncon
hsa-miR-4651 1464-1471 -0.344 91.0 -0.344 93.0 noncon
hsa-miR-654-5p 1219-1225 -0.34 96.0 -0.34 97.0 noncon
hsa-miR-6760-5p 1190-1197 -0.335 98.0 -0.335 99.0 noncon
hsa-miR-3652 1801-1807 -0.327 98.0 -0.327 98.0 noncon
hsa-miR-1301-3p 1954-1960 -0.324 97.0 -0.324 98.0 noncon
hsa-miR-4313 1092-1099 -0.321 94.0 -0.321 96.0 noncon
hsa-miR-4318 1605-1612 -0.32 98.0 -0.32 98.0 noncon
hsa-miR-128-2-5p 807-814 -0.313 97.0 -0.313 98.0 noncon
hsa-miR-211-5p 1169-1176 -0.312 97.0 -0.312 98.0 noncon
hsa-miR-6800-5p 1935-1942 -0.312 97.0 -0.312 98.0 noncon
hsa-miR-204-5p 1169-1176 -0.312 97.0 -0.312 98.0 noncon
hsa-miR-6804-5p 104-110 -0.308 92.0 -0.308 94.0 noncon
hsa-miR-6515-5p 72-79 -0.306 95.0 -0.306 96.0 noncon
hsa-miR-296-5p 1300-1307 -0.306 91.0 -0.306 93.0 noncon
hsa-miR-6506-5p 184-191 -0.296 98.0 -0.296 99.0 noncon
hsa-miR-4779 106-112 -0.295 97.0 -0.295 97.0 noncon
hsa-miR-3175 53-60 -0.294 94.0 -0.294 95.0 noncon
hsa-miR-5047 1954-1960 -0.291 96.0 -0.291 97.0 noncon
hsa-miR-6832-3p 1168-1175 -0.29 97.0 -0.29 98.0 noncon
hsa-miR-4258 686-693 -0.288 92.0 -0.288 94.0 noncon
hsa-miR-6829-5p 485-492 -0.281 94.0 -0.281 95.0 noncon
hsa-miR-524-3p 889-895 -0.276 92.0 -0.276 94.0 noncon
hsa-miR-525-3p 889-895 -0.276 92.0 -0.276 95.0 noncon
hsa-miR-218-5p 174-180 -0.276 94.0 -0.276 96.0 con
hsa-miR-765 733-740 -0.276 93.0 -0.276 94.0 noncon
hsa-miR-3679-5p 1943-1949 -0.27 95.0 -0.27 96.0 noncon
hsa-miR-4316 1789-1796 -0.269 96.0 -0.269 97.0 noncon
hsa-miR-203b-5p 2053-2059 -0.264 94.0 -0.264 96.0 noncon
hsa-miR-4529-5p 236-243 -0.261 90.0 -0.261 93.0 noncon
hsa-miR-5588-5p 148-155 -0.26 96.0 -0.26 97.0 noncon
hsa-miR-134-3p 1604-1610 -0.258 95.0 -0.258 96.0 noncon
hsa-miR-4759 2251-2257 -0.257 95.0 -0.239 96.0 noncon
hsa-miR-3943 122-128 -0.256 92.0 -0.256 94.0 noncon
hsa-miR-6718-5p 2053-2059 -0.253 94.0 -0.253 96.0 noncon
hsa-miR-6865-5p 1647-1653 -0.252 93.0 -0.252 95.0 noncon