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
CHPF



General Information
Gene Symbol:   
CHPF
Protein name:   
Chondroitin sulfate synthase 2
Enzyme Class:   
Sulfate synthase
CAZy Family:   
GT31
E.C. No:   
2.4.1.175
Organs:   
Reaction (SNFG):   
+
→
+ UDP
+
→
+ UDP
Reaction (IUBMB):   
No specified reaction.
About

• The GalNAcT-I activity catalyzes GalNAc transfer toward GlcA in the linkage tetrasaccharide (GlcAβ1-3Galβ1-3Galβ1-4Xylβ1-). This is strongly mediated by CSGalNAcT1 (ChGn1) but can also be performed by CSGalNAcT-II (ChGn2).
• GalNAcT-II catalyzes elongation activity to create repeating disaccharide unit (GlcAβ1-3GalNAcβ1-4)n in the CS chain. This is more readily performed by CSGalNAcT2. Mice lacking CSGalNAcT1 exhibit dwarf phenotype with less cartilage development
• Overall, CSGalNAcT1 and CSGalNAcT2 mediate both initiation and elongation of CS via GalNAcT activity
• CHSY1 (Chondroitin synthase-1/chondroitin sulfate synthase-1 (CSS1)) and CHSY3 (chondroitin synthase-3/chondroitin sulfate synthase-3 (CSS3)) exhibit dual glycosyltransferase activities of β1,3 GlcA-T and β1,4 GalNAc-T for CS initiation and elongation
• CHPF (chondroitin sulfate synthase-2 (CSS2)) also exhibits dual glycosyltransferase activities of β1,3 GlcA-T and β1,4 GalNAc-T for CS initiation and elongation. Its activity is similar to that of CSS1 and CSS3.
• CHPF2 (chondroitin polymerizing factor 2/chondroitin sulfate glucuronyltransferase (CSGlcA-T)) transfers glucuronic acid (GlcUA) from UDP-GlcUA to N-acetylgalactosamine in the elongating chondroitin polymer. It does not have GalNAcT activity.
• CS is also present broadly in the tissues and abundantly in the cartilage and brain. Aggrecan contains abundant CS in cartilage.

Related Pathway
KEGG ORTHOLOGY:   
K00747
KEGG Pathway:   
ko00532  ko01100 
Reactome:   
R-HSA-2022870
Related Database
Organism:   
Homo sapiens
Uniprot:   
Q8IZ52 
NCBI GeneID:   
79586
GlyMap GeneID:   
79586
DNA aRefSeq:   
NM_001195731.1 
Protein RefSeq:   
NP_001182660.1 
BRENDA:   
Kinetic info.
OMIM number:   
610405
GeneCards database:   
CHPF
Enzyme Specificity
Glycan Type:  
     GAG
Compartment:  
     Cis, Medial, Trans, TGN
Substrate:  
     GlcA(b1-3) or GalNAc(b1-4)
Product:  
     GalNAc(b1-4)GlcA(b1-3) or GlcA(b1-3)GalNAc(b1-4)
Constraints:  
     nGlcA(b1-3)Gal(b1-3)Gal(b1-4)Xyl(b1-r)>=1&!IdoA(a1-3)
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 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 200 180 160 140 120 100 80 60 40 20 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-6870-5p 50-57 -0.603 99.0 -0.603 99.0 noncon
hsa-miR-4435 415-422 -0.587 99.0 -0.585 99.0 noncon
hsa-miR-5698 50-57 -0.587 99.0 -0.587 99.0 noncon
hsa-miR-4723-5p 50-57 -0.555 98.0 -0.555 98.0 noncon
hsa-miR-7111-5p 50-57 -0.555 98.0 -0.555 98.0 noncon
hsa-miR-6736-3p 345-352 -0.551 99.0 -0.55 99.0 noncon
hsa-miR-4313 355-362 -0.494 98.0 -0.493 98.0 noncon
hsa-miR-4665-5p 51-58 -0.489 98.0 -0.489 98.0 noncon
hsa-miR-608 39-46 -0.485 97.0 -0.485 97.0 noncon
hsa-miR-4651 39-46 -0.48 97.0 -0.48 97.0 noncon
hsa-miR-6798-5p 224-231 -0.457 98.0 -0.457 99.0 noncon
hsa-miR-637 181-188 -0.455 99.0 -0.455 99.0 noncon
hsa-miR-6793-3p 332-339 -0.436 99.0 -0.435 99.0 noncon
hsa-miR-6728-5p 202-209 -0.414 99.0 -0.414 99.0 noncon
hsa-miR-760 62-69 -0.409 97.0 -0.409 98.0 noncon
hsa-miR-4667-3p 340-347 -0.405 98.0 -0.405 99.0 noncon
hsa-miR-5187-5p 201-208 -0.401 98.0 -0.401 98.0 noncon
hsa-miR-1275 51-58 -0.4 98.0 -0.4 98.0 noncon
hsa-miR-6734-3p 336-343 -0.399 98.0 -0.398 98.0 noncon
hsa-miR-6856-3p 316-323 -0.391 98.0 -0.391 99.0 noncon
hsa-miR-6807-3p 266-273 -0.378 99.0 -0.378 99.0 noncon
hsa-miR-6805-5p 223-229 -0.367 95.0 -0.367 96.0 noncon
hsa-miR-4726-5p 115-122 -0.362 95.0 -0.362 96.0 noncon
hsa-miR-217 266-273 -0.357 99.0 -0.357 99.0 noncon
hsa-miR-125b-2-3p 429-436 -0.344 98.0 0.0 33.0 noncon
hsa-miR-4692 278-285 -0.339 98.0 -0.339 99.0 noncon
hsa-miR-6747-5p 34-41 -0.337 97.0 -0.337 97.0 noncon
hsa-miR-4640-5p 115-122 -0.336 94.0 -0.336 95.0 noncon
hsa-miR-4736 69-76 -0.334 98.0 -0.334 98.0 noncon
hsa-miR-4514 278-285 -0.333 98.0 -0.333 98.0 noncon
hsa-miR-1207-5p 399-405 -0.32 96.0 -0.32 97.0 noncon
hsa-miR-503-5p 232-238 -0.314 98.0 -0.314 99.0 con
hsa-miR-4763-3p 399-405 -0.31 96.0 -0.31 97.0 noncon
hsa-miR-1207-5p 219-225 -0.309 96.0 -0.309 96.0 noncon
hsa-miR-6887-3p 353-359 -0.307 91.0 -0.307 94.0 noncon
hsa-miR-548an 402-409 -0.303 98.0 -0.303 98.0 noncon
hsa-miR-361-3p 169-176 -0.294 96.0 -0.294 97.0 noncon
hsa-miR-5591-5p 395-401 -0.291 93.0 -0.291 95.0 noncon
hsa-miR-940 400-406 -0.289 98.0 -0.289 98.0 noncon
hsa-miR-6808-5p 400-406 -0.285 98.0 -0.285 98.0 noncon
hsa-miR-6893-5p 400-406 -0.285 98.0 -0.285 98.0 noncon
hsa-miR-6819-5p 40-46 -0.282 93.0 -0.282 94.0 noncon
hsa-miR-6836-5p 291-297 -0.279 94.0 -0.279 95.0 noncon
hsa-miR-760 185-192 -0.278 93.0 -0.278 94.0 noncon
hsa-miR-6865-5p 66-72 -0.275 94.0 -0.275 96.0 noncon
hsa-miR-1207-5p 386-392 -0.274 94.0 -0.274 95.0 noncon
hsa-miR-3612 252-258 -0.271 95.0 -0.271 96.0 noncon
hsa-miR-363-5p 190-196 -0.27 94.0 -0.27 95.0 noncon
hsa-miR-6740-5p 205-211 -0.268 93.0 -0.268 95.0 noncon
hsa-miR-6726-5p 395-401 -0.266 91.0 -0.266 93.0 noncon
hsa-miR-4484 403-409 -0.265 98.0 -0.265 98.0 noncon
hsa-miR-6815-5p 66-72 -0.264 94.0 -0.264 96.0 noncon
hsa-miR-6803-5p 52-58 -0.262 93.0 -0.262 94.0 noncon
hsa-miR-6742-5p 41-47 -0.261 93.0 -0.261 95.0 noncon
hsa-miR-6737-5p 40-46 -0.26 92.0 -0.26 93.0 noncon
hsa-miR-650 252-258 -0.259 95.0 -0.259 96.0 noncon
hsa-miR-3175 49-55 -0.259 92.0 -0.259 94.0 noncon
hsa-miR-4300 395-401 -0.258 91.0 -0.258 93.0 noncon
hsa-miR-4763-3p 219-225 -0.255 93.0 -0.255 94.0 noncon
hsa-miR-6751-5p 52-58 -0.253 92.0 -0.253 94.0 noncon
hsa-miR-30c-2-3p 363-370 -0.252 96.0 -0.252 97.0 noncon
hsa-miR-30c-1-3p 363-370 -0.252 96.0 -0.252 97.0 noncon
hsa-miR-6819-5p 35-41 -0.25 90.0 -0.25 92.0 noncon