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
GLCE



General Information
Gene Symbol:   
GLCE
Protein name:   
D-glucuronyl C5-epimerase
Enzyme Class:   
Epimerase
CAZy Family:   
E.C. No:   
5.1.3.17
Organs:   
Reaction (SNFG):   
→
Reaction (IUBMB):   
No specified reaction.
About

• GLCE (C5-epimerase) mediates the conversion of GlcA on HS/heparin to IdoA adjacent to GlcNS N-sulfated sugar residues.
• GLCE can form a complex with HS2ST1 to facilitate conversion of GlcA to IdoA2S.
• Heparin is extensively sulfated and has a high content of IdoA (typically 50-90 % of the total hexuronic acid), whereas HS has a more varied structure, generally less sulfated and with lower IdoA content than heparin (typically 30-55 % of the total hexuronic acid).
• Heparin is only expressed by connective-tissue-type mast cells, whereas HS is produced by all other mammalian (and many nonmammalian) cells.
• GLCE knockout mice exhibit a variety of abnormalities including the lack of kidneys

Related Pathway
KEGG ORTHOLOGY:   
K01793
KEGG Pathway:   
ko00534  ko01100 
Reactome:   
R-HSA-2022928
Related Database
Organism:   
Homo sapiens
Uniprot:   
O94923 
NCBI GeneID:   
26035
GlyMap GeneID:   
26035
DNA aRefSeq:   
NM_001324093.1 
Protein RefSeq:   
NP_001311022.1 
BRENDA:   
Kinetic info.
OMIM number:   
612134
GeneCards database:   
GLCE
Enzyme Specificity
Glycan Type:  
     GAG
Compartment:  
     Cis, Medial, Trans, TGN
Substrate:  
     ...GlcA(b1-4)
Product:  
     ...IdoA(a1-4)
Constraints:  
     !GlcNAc(a1-4)@GlcA(b1-4)Gal(b1-3)Gal(b1-4)Xyl(b1-r)&!GlcNAc(a1-4)GlcA(b1-4)GlcN(a1-4 NS-2)
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
ENST00000261858 ENST00000559420 ENST00000559798
miRNA-GlycoEnzyme Interactome {ref. 9}
miRNA Name Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
hsa-miR-4746-5p 1341-1348 -0.493 94.0 -0.346 89.0 noncon
hsa-miR-218-5p 643-650 -0.481 99.0 -0.338 97.0 con
hsa-miR-218-5p 2808-2815 -0.441 98.0 -0.124 85.0 con
hsa-miR-4313 1499-1506 -0.434 97.0 -0.306 95.0 noncon
hsa-miR-4999-5p 2836-2843 -0.419 97.0 -0.119 83.0 noncon
hsa-miR-4771 2171-2178 -0.393 97.0 -0.156 87.0 noncon
hsa-miR-4435 325-332 -0.391 98.0 -0.391 98.0 noncon
hsa-miR-5685 221-228 -0.39 99.0 -0.39 99.0 noncon
hsa-miR-6866-5p 2267-2274 -0.384 96.0 -0.153 87.0 noncon
hsa-miR-6842-3p 2486-2493 -0.349 97.0 -0.14 85.0 noncon
hsa-miR-4725-3p 1772-1779 -0.347 96.0 -0.14 80.0 noncon
hsa-miR-6780b-5p 1772-1779 -0.347 96.0 -0.14 79.0 noncon
hsa-miR-6846-5p 1201-1208 -0.345 92.0 -0.246 87.0 noncon
hsa-miR-6848-5p 1201-1208 -0.345 92.0 -0.246 86.0 noncon
hsa-miR-218-5p 2597-2604 -0.336 97.0 -0.135 86.0 con
hsa-miR-370-5p 1375-1382 -0.335 98.0 -0.239 96.0 noncon
hsa-miR-324-3p 1501-1508 -0.333 97.0 -0.237 95.0 noncon
hsa-miR-302c-3p.2 1455-1462 -0.329 97.0 -0.235 95.0 noncon
hsa-miR-4271 1772-1779 -0.327 97.0 -0.132 86.0 noncon
hsa-miR-6834-3p 854-860 -0.325 96.0 -0.232 93.0 noncon
hsa-miR-147b 1180-1186 -0.318 93.0 -0.227 87.0 noncon
hsa-miR-1913 1501-1508 -0.315 97.0 -0.225 94.0 noncon
hsa-miR-1193 1375-1382 -0.314 97.0 -0.224 95.0 noncon
hsa-miR-4716-3p 947-953 -0.307 92.0 -0.22 86.0 noncon
hsa-miR-520f-3p 1455-1462 -0.305 96.0 -0.218 94.0 noncon
hsa-miR-582-5p 2931-2938 -0.298 97.0 -0.087 86.0 noncon
hsa-miR-4690-3p 221-228 -0.296 99.0 -0.296 99.0 noncon
hsa-miR-449a 1980-1986 -0.296 91.0 -0.12 73.0 con
hsa-miR-34a-5p 1980-1986 -0.285 90.0 -0.116 72.0 con
hsa-miR-4703-3p 2276-2283 -0.278 95.0 -0.113 82.0 noncon
hsa-miR-7110-3p 839-846 -0.275 91.0 -0.197 90.0 noncon
hsa-miR-4433b-5p 853-859 -0.274 93.0 -0.197 90.0 noncon
hsa-miR-20b-3p 2278-2285 -0.271 96.0 -0.111 88.0 noncon
hsa-miR-3622a-5p 1887-1893 -0.27 97.0 -0.11 89.0 noncon
hsa-miR-124-5p 202-208 -0.267 93.0 -0.267 95.0 noncon
hsa-miR-4693-5p 1609-1616 -0.266 95.0 -0.191 93.0 noncon
hsa-miR-4314 2021-2028 -0.266 94.0 -0.109 79.0 noncon
hsa-miR-124-3p.1 1888-1895 -0.264 93.0 -0.108 87.0 con
hsa-miR-497-5p 2655-2661 -0.262 93.0 -0.107 82.0 con
hsa-miR-892a 433-440 -0.262 96.0 -0.262 97.0 noncon
hsa-miR-1236-5p 286-292 -0.262 94.0 -0.262 96.0 noncon
hsa-miR-455-5p 73-79 -0.261 93.0 -0.261 95.0 noncon
hsa-miR-4283 1200-1206 -0.26 91.0 -0.187 88.0 noncon
hsa-miR-4305 785-792 -0.257 91.0 -0.185 87.0 noncon
hsa-miR-6838-5p 2655-2661 -0.254 92.0 -0.104 80.0 con
hsa-miR-4524a-3p 55-62 -0.253 94.0 -0.253 96.0 noncon
hsa-miR-4693-5p 434-441 -0.253 94.0 -0.253 96.0 noncon
hsa-miR-424-5p 2655-2661 -0.25 92.0 -0.102 81.0 con