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
XYLT2



General Information
Gene Symbol:   
XYLT2
Protein name:   
Xylosyltransferase 2
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:   
Q9H1B5 
NCBI GeneID:   
64132
GlyMap GeneID:   
64132
DNA aRefSeq:   
NM_022167.3 
Protein RefSeq:   
NP_071450.2 
BRENDA:   
Kinetic info.
OMIM number:   
608125
GeneCards database:   
XYLT2
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 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 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-3181 541-548 -0.606 97.0 -0.585 98.0 noncon
hsa-miR-4735-3p 40-47 -0.568 99.0 -0.568 99.0 con
hsa-miR-6749-5p 540-547 -0.553 98.0 -0.534 98.0 noncon
hsa-miR-18a-5p 40-47 -0.518 99.0 -0.518 99.0 con
hsa-miR-18b-5p 40-47 -0.518 99.0 -0.518 99.0 con
hsa-miR-367-5p 830-837 -0.479 99.0 -0.457 99.0 noncon
hsa-miR-6715b-5p 798-805 -0.422 99.0 -0.408 99.0 noncon
hsa-miR-4258 196-203 -0.405 97.0 -0.405 98.0 noncon
hsa-miR-1233-3p 356-363 -0.399 98.0 -0.386 98.0 noncon
hsa-miR-6811-3p 73-80 -0.396 98.0 -0.396 98.0 noncon
hsa-miR-4455 230-237 -0.368 94.0 -0.368 95.0 noncon
hsa-miR-25-3p 349-356 -0.357 97.0 -0.345 98.0 con
hsa-miR-363-3p 349-356 -0.346 97.0 -0.335 97.0 con
hsa-miR-6752-3p 136-143 -0.346 96.0 -0.346 97.0 noncon
hsa-miR-6793-5p 123-130 -0.344 96.0 -0.344 97.0 noncon
hsa-miR-4269 798-805 -0.344 99.0 -0.333 99.0 noncon
hsa-miR-5008-5p 462-469 -0.331 96.0 -0.32 97.0 noncon
hsa-miR-367-3p 349-356 -0.33 97.0 -0.319 97.0 con
hsa-miR-32-5p 349-356 -0.328 97.0 -0.318 97.0 con
hsa-miR-4455 101-108 -0.321 91.0 -0.321 93.0 noncon
hsa-miR-92b-3p 349-356 -0.32 97.0 -0.31 97.0 con
hsa-miR-92a-3p 349-356 -0.32 97.0 -0.31 97.0 con
hsa-miR-448 826-833 -0.313 97.0 -0.303 98.0 con
hsa-miR-6886-3p 210-217 -0.31 94.0 -0.31 95.0 noncon
hsa-miR-499b-5p 817-824 -0.307 97.0 -0.297 97.0 noncon
hsa-miR-7156-3p 514-521 -0.305 96.0 -0.295 97.0 noncon
hsa-miR-508-5p 787-794 -0.3 98.0 -0.29 98.0 noncon
hsa-miR-3944-5p 97-104 -0.299 96.0 -0.299 97.0 noncon
hsa-miR-194-3p 691-698 -0.288 97.0 -0.279 97.0 noncon
hsa-miR-1247-3p 29-35 -0.283 91.0 -0.283 94.0 noncon
hsa-miR-4532 29-35 -0.277 91.0 -0.277 93.0 noncon
hsa-miR-6793-3p 179-186 -0.274 97.0 -0.274 98.0 noncon
hsa-miR-892a 150-157 -0.274 96.0 -0.274 97.0 noncon
hsa-miR-4524b-3p 253-260 -0.273 99.0 -0.264 99.0 noncon
hsa-miR-1825 723-730 -0.27 96.0 -0.262 97.0 noncon
hsa-miR-6852-5p 370-377 -0.267 96.0 -0.259 97.0 noncon
hsa-miR-3151-3p 184-191 -0.263 93.0 -0.263 95.0 noncon
hsa-miR-1199-5p 358-365 -0.259 95.0 -0.251 96.0 noncon
hsa-miR-331-3p 608-615 -0.258 96.0 -0.25 97.0 con