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}
GLCE/hsa-miR-4305
miRNA Target Site Type Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
5'...UUUUUGUCAC UGUCUAGA ...
3'   CUUGACCUCC ACAGAUC C
 8mer 785-792 -0.257 91.0 -0.185 87.0 noncon
5'...ACUGGCCAAC UGUCUAG C...
3'   CUUGACCUCC ACAGAUC C
 7mer-m8 334-340 -0.115 62.0 -0.115 77.0 noncon