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
CHST13



General Information
Gene Symbol:   
CHST13
Protein name:   
Carbohydrate sulfotransferase 13
Enzyme Class:   
Sulfate synthase
CAZy Family:   
E.C. No:   
2.8.2.5
Organs:   
Reaction (SNFG):   
PAPS +
→
+ PAP
Reaction (IUBMB):   
No specified reaction.
About

• Chondroitin sulfate chains are composed of GlcAβ1-3GalNAcβ1-4 repeating unit. Various sulfotransferases, CHST3, 7, 11-13, 14, 15, and UST, sulfate either GalNAc and GlcA residues. CS are a major functional component of aggrecan, and needed for cartilage formation and maintenance.
• CHST11-13 are three isoforms of the C4ST family, C4ST-1, C4ST-2 and C4ST-3.
• These enzymes transfer sulfate from PAPS donor to C4 of GalNAc on CS chains.
• CHST11 transfer sulfate to GalNAc residue adjacent to the reducing side of the GlcA, and also at the non-reducing end. Chondroitin 4-sulfate formed by C4STs serve as acceptors for GalNAc4S-6ST to form chondroitin sulfate E.
• CHST12 acts on GalNAc adjacent not only to GlcA but also IdoA in desulfated dermatan sulfate. The activity for the latter is lower.
• CHST13 displays similar activity to CHST11

Related Pathway
KEGG ORTHOLOGY:   
K07779
KEGG Pathway:   
ko00532 
Reactome:   
R-HSA-2022870
Related Database
Organism:   
Homo sapiens
Uniprot:   
Q3SYA3 
NCBI GeneID:   
166012
GlyMap GeneID:   
166012
DNA aRefSeq:   
NM_152889.2 
Protein RefSeq:   
NP_690849.1 
BRENDA:   
Kinetic info.
OMIM number:   
610124
GeneCards database:   
CHST13
Enzyme Specificity
Glycan Type:  
     GAG
Compartment:  
     Cis, Medial, Trans, TGN
Substrate:  
     GlcA(b1-3)GalNAc(b1-4)GlcA(b1-3)
Product:  
     GlcA(b1-3)GalNAc(b1-4 [4S])GlcA(b1-3)
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 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 10 8 6 4 2 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-5587-3p 53-60 -0.622 99.0 -0.622 99.0 noncon
hsa-miR-6763-3p 54-61 -0.525 98.0 -0.525 98.0 noncon
hsa-miR-4649-5p 414-421 -0.513 96.0 -0.513 97.0 noncon
hsa-miR-6859-3p 321-328 -0.491 98.0 -0.491 98.0 noncon
hsa-miR-6729-5p 414-421 -0.481 96.0 -0.481 96.0 noncon
hsa-miR-1915-5p 275-282 -0.465 98.0 -0.465 98.0 noncon
hsa-miR-128-1-5p 74-81 -0.455 98.0 -0.455 99.0 noncon
hsa-miR-566 562-569 -0.422 98.0 -0.422 98.0 noncon
hsa-miR-34c-5p 515-522 -0.398 96.0 -0.398 97.0 noncon
hsa-miR-1204 19-25 -0.397 94.0 -0.397 96.0 noncon
hsa-miR-34a-5p 515-522 -0.388 96.0 -0.388 97.0 noncon
hsa-miR-449b-5p 515-522 -0.382 95.0 -0.382 96.0 noncon
hsa-miR-3622b-5p 610-617 -0.372 98.0 -0.372 98.0 noncon
hsa-miR-128-2-5p 74-81 -0.366 98.0 -0.366 98.0 noncon
hsa-miR-449a 515-522 -0.364 95.0 -0.364 96.0 noncon
hsa-miR-767-5p 350-357 -0.359 98.0 -0.359 98.0 noncon
hsa-miR-1915-5p 426-433 -0.35 95.0 -0.35 97.0 noncon
hsa-miR-214-5p 246-253 -0.342 98.0 -0.342 98.0 noncon
hsa-miR-6825-5p 405-412 -0.341 92.0 -0.341 94.0 noncon
hsa-miR-5006-5p 423-430 -0.328 96.0 -0.328 97.0 noncon
hsa-miR-1247-3p 487-494 -0.326 95.0 -0.326 96.0 noncon
hsa-miR-1207-3p 240-247 -0.324 98.0 -0.324 98.0 noncon
hsa-miR-6895-5p 551-558 -0.323 97.0 -0.323 97.0 noncon
hsa-miR-8085 537-544 -0.316 96.0 -0.316 97.0 noncon
hsa-miR-6731-5p 537-544 -0.316 96.0 -0.316 97.0 noncon
hsa-miR-3655 43-50 -0.314 99.0 -0.314 99.0 noncon
hsa-miR-6756-5p 418-424 -0.299 90.0 -0.299 92.0 noncon
hsa-miR-4787-5p 50-56 -0.297 93.0 -0.297 94.0 noncon
hsa-miR-4283 621-627 -0.289 93.0 -0.289 94.0 noncon
hsa-miR-504-5p.1 291-297 -0.278 98.0 -0.278 98.0 noncon
hsa-miR-7847-3p 228-234 -0.274 92.0 -0.274 94.0 noncon
hsa-miR-6829-5p 164-171 -0.274 94.0 -0.274 95.0 noncon
hsa-miR-5588-3p 653-659 -0.273 95.0 -0.273 96.0 noncon
hsa-miR-502-3p 352-358 -0.257 94.0 -0.257 96.0 noncon
hsa-miR-501-3p 352-358 -0.257 94.0 -0.257 96.0 noncon
hsa-miR-548as-3p 294-301 -0.256 98.0 -0.256 98.0 noncon
hsa-miR-212-5p 442-449 -0.252 94.0 -0.252 95.0 noncon
hsa-miR-6732-3p 292-298 -0.251 95.0 -0.251 97.0 noncon
hsa-miR-6132 181-188 -0.251 91.0 -0.251 93.0 noncon