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
ALG12



General Information
Gene Symbol:   
ALG12
Protein name:   
Dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase
Enzyme Class:   
Glycosyltransferase
CAZy Family:   
GT22
E.C. No:   
2.4.1.260
Organs:   
Reaction (SNFG):   
+
→
+ P-Dol
Reaction (IUBMB):   
No specified reaction.
About

• Extension of Man5GlcNAc2-P-P-Dol in the ER lumen involves the addition of four Man (by ALG3 [α(1,3)ManT], ALG9 [α(1,2)ManT], ALG12 [α(1,6)ManT] followed by ALG9 [α(1,2)ManT] again) and three Glc residues (by ALG6 [α(1,3)GlcT], ALG8 [α(1,3)GlcT] and ALG10 [α(1,2)GlcT]).
• In all instances the transfer uses either Dol-P-Man or Dol-P-Glc as donor.
• Dol-P-Man is formed from GDP-Man using enzymes DPM1,2,3
• Dol-P-Glc is formed from UDP-Glc using ALG5

Related Pathway
KEGG ORTHOLOGY:   
K03847
KEGG Pathway:   
ko00510  ko00513  ko01100 
Reactome:   
R-HSA-446193
Related Database
Organism:   
Homo sapiens
Uniprot:   
Q9BV10 
NCBI GeneID:   
79087
GlyMap GeneID:   
79087
DNA aRefSeq:   
NM_024105.3 
Protein RefSeq:   
NP_077010.1 
BRENDA:   
Kinetic info.
OMIM number:   
607144
GeneCards database:   
ALG12
Enzyme Specificity
Glycan Type:  
     N-linked
Compartment:  
     ER
Substrate:  
     Man(a1-2)Man(a1-3)Man(a1-6)
Product:  
     Man(a1-2)Man(a1-3)[Man(a1-6)]Man(a1-6)
Constraints:  
     nMan=7&nMan(a1-6)=1
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 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
ENST00000330817 ZNF143 BCL6 PPARG TAL1 PPARG TFAP2C PPARG CTCF NFE2 ZBED5 REST USF2 PPARG PRDM14 E2F6 GATA1 REST AR KLF4 ZNF48 ZNF48 CTCFL MYCN BACH1 ZFX NR2F1 SMAD2 NONO TCF3 GATA4 TAF1 TAF1 E2F6 KLF9 EGR1 CEBPD EGR3 ZNF341 TFAP2A ERG GLIS1 GLIS1 PBX3 CTCF FOS NEUROD1 NFYB NFYC E2F6 IRF3 IRF3 SP2 ATF1 RFX5 AR SOX9 SP4 MXI1 MNT EGR2 CTCF MAF MAF E2F4 MAZ KLF15 BCL11B EGR1 KLF12 MYCN USF2 RBPJ SOX17 KLF1 STAT5B TFAP2C USF1 USF1 REST KLF9 CREM CREM SP5 ZNF792 SP3 ZNF35 BCL11B RFXANK PBX3 PBX3 THAP1 ATF1 FOXA3 GATAD1 PPARG PPARG THAP11 NFYC TEAD1 CEBPB ZBTB48 RXRB RUNX3 ZSCAN9
miRNA-GlycoEnzyme Interactome {ref. 9}
ALG12/hsa-miR-6756-5p
miRNA Target Site Type Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
5'... CCACGUGUGUCCUG CCCACCCA ...
3'   UCGGGGUGGAGGUCG GGGUGGG A
 8mer 364-371 -0.292 90.0 -0.292 92.0 noncon
5'... CCCGGCCGCACCCC CCCACCC U...
3'   UCGGGGUGGAGGUCG GGGUGGG A
 7mer-m8 482-488 -0.179 68.0 -0.179 77.0 noncon
5'... UUGCACGGUUCUCC CCCACCC C...
3'   UCGGGGUGGAGGUCG GGGUGGG A
 7mer-m8 3104-3110 -0.117 53.0 -0.004 23.0 noncon