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

NDST3



General Information
Gene Symbol:   
NDST3
Protein name:   
Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3
Enzyme Class:   
Sulfate synthase
CAZy Family:   
E.C. No:   
Organs:   
Reaction (SNFG):   
PAPS +
+ PAP
Reaction (IUBMB):   
No specified reaction.

About

• Heparan sulfate (HS) are expressed on all vertebrate cells as part of HS proteoglycans. Common HSPGs include perlecan, agrin, and collagen XVIII that are part of basement membranes, and cell surface syndecans and glypicans. Many growth factors, morphogens, chemokines, and cytokines are presented by the HS. Thus, HS are critical part of embryonic development and adult hemostasis.
• The first committed HS chain modification is catalyzed by one of four NDST isoforms, present in the medial and trans-Golgi. These are bifunctional enzymes that first N-deacetylase GlcNAc to generate free amino groups, followed by sulfation.
• All subsequent modification (GlcA->IdoA epimerization, O-sulfation etc.) depends on N-sulfation status except for 6-O-sulfation, which is NS-status independent. Heavily sulfated domains that are functional typically contain IdoA rather than GlcA.
• NDST1 and NDST2 showed display high deacetylase and sulfotransferase activities. NDST3 shows relatively higher deacetylase activities but low sulfotransferase activity. NDST4 has high sulfotransferase activities but low deacetylase activities.
• NDST1 & NDST2 are important enzyme mediating N-sulfation as they are widely expressed. They play a critical role in regulating cell signaling by facilitating the binding of various growth factors.
• Due to their restricted expression profile, NDST3 and NDST4 have a less penetrating impact on biological function.


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:  
     GAG
Compartment:  
     Cis, Medial, Trans, TGN
Substrate:  
     GlcA(b1-4)GlcNAc(a1-4)GlcA(b1-4)
Product:  
     GlcA(b1-4)GlcN(a1-4 [NS])GlcA(b1-4)
Constraints:  
     var=50%

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 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 2 0 Transcripts per million (TPM)
Transcription factor {ref. 10}
No high degree of confidence data

miRNA-GlycoEnzyme Interactome {ref. 9}
NDST3/hsa-miR-6510-5p
miRNA Target Site Type Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
5'...GUAGUAAAUUAAUU CCCUGCUA ...
3'   CUGAGGAGAGAGAG GGGACGA C
8mer 1781-1788 -0.329 98.0 -0.329 98.0 noncon