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

NDST2



General Information
Gene Symbol:   
NDST2
Protein name:   
Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 2
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 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 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-133a-5p 16-23 -0.639 99.0 -0.639 99.0 noncon
hsa-miR-4646-3p 168-175 -0.486 99.0 -0.486 99.0 noncon
hsa-miR-6846-5p 113-120 -0.483 97.0 -0.483 98.0 noncon
hsa-miR-6729-3p 448-455 -0.464 99.0 -0.445 99.0 noncon
hsa-miR-4458 103-110 -0.459 97.0 -0.459 98.0 con
hsa-miR-4433b-5p 167-174 -0.455 98.0 -0.455 99.0 noncon
hsa-miR-6848-5p 113-120 -0.443 96.0 -0.443 97.0 noncon
hsa-miR-6741-3p 474-481 -0.438 98.0 -0.42 98.0 noncon
hsa-let-7d-5p 103-110 -0.435 96.0 -0.435 97.0 con
hsa-let-7a-5p 103-110 -0.417 96.0 -0.417 97.0 con
hsa-let-7c-5p 103-110 -0.417 96.0 -0.417 97.0 con
hsa-let-7b-5p 103-110 -0.417 96.0 -0.417 97.0 con
hsa-let-7e-5p 103-110 -0.417 96.0 -0.417 97.0 con
hsa-miR-4265 64-71 -0.414 98.0 -0.414 98.0 noncon
hsa-miR-1257 434-441 -0.41 99.0 -0.394 99.0 noncon
hsa-let-7i-5p 103-110 -0.409 96.0 -0.409 97.0 con
hsa-let-7g-5p 103-110 -0.409 95.0 -0.409 97.0 con
hsa-let-7f-5p 103-110 -0.409 95.0 -0.409 97.0 con
hsa-miR-98-5p 103-110 -0.409 95.0 -0.409 97.0 con
hsa-miR-4500 103-110 -0.409 96.0 -0.409 97.0 con
hsa-miR-5088-5p 486-493 -0.401 98.0 -0.385 99.0 noncon
hsa-miR-1287-3p 500-507 -0.4 96.0 -0.384 97.0 noncon
hsa-miR-1265 521-527 -0.398 99.0 -0.382 99.0 noncon
hsa-miR-4296 64-71 -0.387 98.0 -0.387 98.0 noncon
hsa-miR-4322 64-71 -0.358 97.0 -0.358 98.0 noncon
hsa-miR-6742-5p 195-202 -0.347 97.0 -0.333 97.0 noncon
hsa-miR-492 49-56 -0.335 94.0 -0.335 96.0 noncon
hsa-miR-6749-3p 244-251 -0.333 95.0 -0.32 96.0 noncon
hsa-miR-6805-5p 28-34 -0.331 92.0 -0.331 94.0 noncon
hsa-miR-8080 509-516 -0.323 98.0 -0.31 98.0 noncon
hsa-miR-4756-5p 422-429 -0.318 97.0 -0.306 98.0 noncon
hsa-miR-299-3p 197-204 -0.317 97.0 -0.305 97.0 noncon
hsa-miR-6762-5p 381-387 -0.314 92.0 -0.302 93.0 noncon
hsa-miR-6724-5p 62-68 -0.314 95.0 -0.314 96.0 noncon
hsa-miR-6773-5p 62-68 -0.306 94.0 -0.306 96.0 noncon
hsa-miR-6775-3p 60-66 -0.304 93.0 -0.304 95.0 noncon
hsa-miR-6752-3p 264-270 -0.299 94.0 -0.288 95.0 noncon
hsa-miR-4739 422-429 -0.299 96.0 -0.288 97.0 noncon
hsa-miR-6845-5p 381-387 -0.292 90.0 -0.281 92.0 noncon
hsa-miR-138-5p 17-23 -0.286 92.0 -0.286 94.0 noncon
hsa-miR-1291 60-66 -0.281 92.0 -0.281 94.0 noncon
hsa-miR-6769a-3p 179-185 -0.28 98.0 -0.28 98.0 noncon
hsa-miR-3162-5p 423-430 -0.278 92.0 -0.267 94.0 noncon
hsa-miR-6892-3p 253-259 -0.274 94.0 -0.264 95.0 noncon
hsa-miR-4650-5p 120-127 -0.274 97.0 -0.274 97.0 noncon
hsa-miR-1321 422-429 -0.27 95.0 -0.26 96.0 noncon
hsa-miR-6131 17-23 -0.267 97.0 -0.267 98.0 noncon
hsa-miR-1254 260-267 -0.258 96.0 -0.248 97.0 noncon
hsa-miR-4717-5p 83-89 -0.257 95.0 -0.257 97.0 noncon
hsa-miR-6799-3p 59-65 -0.254 93.0 -0.254 95.0 noncon