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
XYLT1



General Information
Gene Symbol:   
XYLT1
Protein name:   
Xylosyltransferase 1
Enzyme Class:   
Glycosyltransferase
CAZy Family:   
GT14
E.C. No:   
2.4.2.26
Organs:   
Reaction (SNFG):   
+ Ser →
+ UDP
Reaction (IUBMB):   
No specified reaction.
About

• Heparan sulfates [HS; sulfated GlcNAc(α1-4)GlcA/IdoA(β1-4)] and chondroitin/dermatan sulfates [CS; sulfated GalNAc(β1-4)GlcA/IdoA(β1-3)] are produced on a common GAG core: GlcA(β1-3)Gal(β1-3)Gal(β1-4)Xylβ-O-Ser.
• This core is synthesized by XYLT1/2, B4GalT-7 ('Gal transferase-I'), B3GalT6 ('Gal transferase-II') and B3GAT3 ('GlcA transferase-I').
• Thus, XYLT1/2 initiate the formation of heparan sulfates, chondroitin sulfates and dermatan sulfates.
• XYLTs are typical Type II enzymes with catalytic activity in the Golgi lumen. It is mostly expressed in Cis-Golgi but some activity may be present in late ER.
• Consensus sequence for XYLT1/2 include Serine with include Ser-Gly and a cluster of nearby acidic residues (e.g. Q-E-E-E-G-S-G-G-G-Q-K).
• XYLT2 is ubiquitously expressed. XYLT1 is rarely expressed alone with the possible exception of cartilage derived cells. Many tissue like kidney, brain, spleen, skeletal muscle etc. express both enzymes.
• XylT2 mice are viable, but develop biliary cysts and renal tubule dilation with accompanied liver and renal fibrosis at 4-5 months.

Related Pathway
KEGG ORTHOLOGY:   
K00771
KEGG Pathway:   
ko00532  ko00534  ko01100 
Reactome:   
R-HSA-1971475
Related Database
Organism:   
Homo sapiens
Uniprot:   
Q86Y38 
NCBI GeneID:   
64131
GlyMap GeneID:   
64131
DNA aRefSeq:   
NM_022166.3 
Protein RefSeq:   
NP_071449.1 
BRENDA:   
Kinetic info.
OMIM number:   
608124
GeneCards database:   
XYLT1
Enzyme Specificity
Glycan Type:  
     GAG
Compartment:  
     
Substrate:  
     Ser
Product:  
     Xyl(b1-r):Ser
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 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
ENST00000261381 TP73 FOXH1 PPARG MAX TCF12 CTCF CEBPA KMT2B RXRA NFIC ZNF263 RCOR1 FOSL2 RUNX1 TCF12 EBF3 MAX PBX3 BHLHE40 ASCL1 MYOD1 RELB AR PPARG FLI1 ZNF335 IKZF1 PPARG ZNF320 FOXP1 FLI1 PKNOX1 SP3 EGR2 MAZ EGR3 KLF15 SP4 VEZF1 SP1
miRNA-GlycoEnzyme Interactome {ref. 9}
miRNA Name Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
hsa-miR-296-5p 3779-3786 -0.425 96.0 -0.425 97.0 noncon
hsa-miR-6893-3p 24-31 -0.359 97.0 -0.359 98.0 noncon
hsa-miR-6880-5p 5174-5181 -0.309 94.0 -0.309 95.0 noncon
hsa-miR-6762-3p 44-51 -0.304 95.0 -0.304 96.0 noncon
hsa-miR-6821-5p 1799-1806 -0.297 94.0 -0.297 96.0 noncon
hsa-miR-18b-5p 6131-6137 -0.286 95.0 -0.286 97.0 con
hsa-miR-18a-5p 6131-6137 -0.286 95.0 -0.286 97.0 con
hsa-miR-6786-5p 3094-3101 -0.28 90.0 -0.28 92.0 noncon
hsa-miR-6893-3p 158-164 -0.269 95.0 -0.269 96.0 noncon
hsa-miR-4735-3p 6131-6137 -0.265 94.0 -0.265 96.0 con
hsa-miR-370-3p 24-31 -0.262 97.0 -0.262 97.0 noncon
hsa-miR-626 3716-3723 -0.261 90.0 -0.261 93.0 noncon
hsa-miR-6734-3p 1197-1203 -0.258 94.0 -0.258 95.0 noncon
hsa-miR-544a 6242-6249 -0.254 94.0 -0.254 96.0 noncon
hsa-miR-450a-1-3p 2785-2791 -0.254 96.0 -0.254 97.0 noncon
hsa-miR-5580-5p 4173-4180 -0.25 91.0 -0.25 93.0 noncon