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

MGAT5B



General Information
Gene Symbol:   
MGAT5B
Protein name:   
Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B
Enzyme Class:   
Glycosyltransferase
CAZy Family:   
E.C. No:   
Organs:   
Reaction (SNFG):   
+
+ UDP
Reaction (IUBMB):   
No specified reaction.

About

• ~30 % of all O-linked glycans in the brain are O-mannose based. This is initiated by protein O-mannosyltransferase 1 (POMT1) and POMT 2, followed by POMGnT1 activity.
• A brain-specific β1,6-N-GlcNAcT (MGAT5B) has been cloned that transfers β1,6GlcNAc to a-mannose in GlcNAc-β1,2-Man-a sequence on both N-glycans and O-mannosyl glycans. In vivo this enzyme is dominantly considered to act on o-mannose glycans of the brain.
• Due to its activity, a variety of extended structures can be formed on the O-mannose backbone including sialylated glycans, glycans with HNK-1 epitope, and those with Lewis X structures.


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 (other)
Compartment:  
     Cis, Medial, Trans, TGN
Substrate:  
     GlcNAc(b1-2)Man(a1-?)Ser|Thr
Product:  
     GlcNAc(b1-2)[GlcNAc(b1-6)]Man(a1-?)Ser|Thr

Simulation Parameters
Mechaelis-Menten parameters (suggested)
VM:    1.00e-05    (pmol/cell • hr)       KM:    1.30e+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 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 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
ENST00000428789 ENST00000565043 ENST00000565675 ENST00000568598 POU5F1 MYCN GRHL2


miRNA-GlycoEnzyme Interactome {ref. 9}
MGAT5B/hsa-miR-6850-3p
miRNA Target Site Type Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
5'...GGCUUUGUGCAA GGCCGGA U...
3'   UCACGCCGCAAGG CCGGCC C
7mer-A1 322-328 -0.273 91.0 -0.273 93.0 noncon
5'...GCAACCCCCCCA GGCCGGA G...
3'   UCACGCCGCAAGG CCGGCC C
7mer-A1 110-116 -0.256 89.0 -0.256 92.0 noncon