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
CHST12



General Information
Gene Symbol:   
CHST12
Protein name:   
Carbohydrate sulfotransferase 12
Enzyme Class:   
Sulfate synthase
CAZy Family:   
E.C. No:   
2.8.2.5
Organs:   
Reaction (SNFG):   
PAPS +
→
+ PAP
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:   
K04742
KEGG Pathway:   
ko00532 
Reactome:   
R-HSA-2022870
Related Database
Organism:   
Homo sapiens
Uniprot:   
Q9NRB3 
NCBI GeneID:   
55501
GlyMap GeneID:   
55501
DNA aRefSeq:   
NM_001243794.1 
Protein RefSeq:   
NP_001230723.1 
BRENDA:   
Kinetic info.
OMIM number:   
610129
GeneCards database:   
CHST12
Enzyme Specificity
Glycan Type:  
     GAG
Compartment:  
     Cis, Medial, Trans, TGN
Substrate:  
     GlcA(b1-3)GalNAc(b1-4)GlcA(b1-3) or GlcA(b1-3)GalNAc(b1-4)IdoA(a1-3)
Product:  
     GlcA(b1-3)GalNAc(b1-4 [4S])GlcA(b1-3) or GlcA(b1-3)GalNAc(b1-4 [4S])IdoA(a1-3)
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 60 50 40 30 20 10 0 Transcripts per million (TPM)
Transcription factor {ref. 10}
Transcriptional start site (TSS) 0 200 -2000 -1800 -1600 -1400 -1200 -1000 -800 -600 -400 -200
ENST00000258711 ENST00000313156 ENST00000618655 USF2 KLF4 ARNT RUNX2
miRNA-GlycoEnzyme Interactome {ref. 9}
CHST12/hsa-miR-1827
miRNA Target Site Type Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
5'...GUUCACUCCA CUGCCUC U...
3'   UAAGUUAGAU GACGGAG U
 7mer-m8 105-111 -0.376 98.0 -0.375 98.0 noncon
5'...GCUGAUGGAG CUGCCUC C...
3'   UAAGUUAGAU GACGGAG U
 7mer-m8 314-320 -0.02 21.0 0.0 18.0 noncon