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

CHPF2



General Information
Gene Symbol:   
CHPF2
Protein name:   
Chondroitin sulfate glucuronyltransferase
Enzyme Class:   
Sulfate synthase
CAZy Family:   
E.C. No:   
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:   
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(b1-3) or GalNAc(b1-4)
Product:  
     GalNAc(b1-4)GlcA(b1-3) or GlcA(b1-3)GalNAc(b1-4)
Constraints:  
     nGalNAc(b1-4)GlcA(b1-3)Gal(b1-3)Gal(b1-4)Xyl(b1-r)>=1

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 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}
CHPF2/hsa-miR-3120-3p
miRNA Target Site Type Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
5'...AGAUAGAGAAUUG UUGCUGUA ...
3'   ACGGACAGAUGUG AACGACA C
8mer 91-98 -0.467 99.0 -0.453 99.0 noncon