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
 
Glycogene class
ABO
ALG1
ALG10
ALG10B
ALG11
ALG12
ALG13
ALG14
ALG1L
ALG1L2
ALG2
ALG3
ALG5
ALG6
ALG8
ALG9
B3GALNT2
B3GALT2
B3GAT1
B3GAT2
B3GNT2
B3GNT4
B3GNT7
B3GNT8
B4GALNT2
B4GALNT3
B4GALNT4
B4GALT1
B4GALT2
B4GALT3
B4GALT4
B4GALT5
CHST1
CHST10
CHST2
CHST3
CHST4
CHST5
CHST8
CHST9
CMAS
CTBS
DAD1
DDOST
DPAGT1
DPM1
DPM2
DPM3
EDEM1
EDEM2
EDEM3
ENGASE
FPGT
FUCA1
FUT1
FUT10
FUT11
FUT2
FUT3
FUT4
FUT5
FUT6
FUT7
FUT8
FUT9
GAL3ST2
GAL3ST3
GANAB
GCNT2
GNPNAT1
GNPTAB
GNPTG
MAN1A1
MAN1A2
MAN1B1
MAN1C1
MAN2A1
MAN2A2
MAN2B1
MAN2B2
MAN2C1
MANBA
MANEA
MGAT1
MGAT2
MGAT3
MGAT4A
MGAT4B
MGAT4C
MGAT4D
MGAT5
MOGS
NAGK
NAGPA
NEU1
NEU2
NEU3
NEU4
PRKCSH
RPN1
RPN2
ST3GAL3
ST3GAL4
ST3GAL6
ST6GAL1
ST6GAL2
ST8SIA2
ST8SIA3
ST8SIA4
STT3A
STT3B
UGGT1
UGGT2
Pathway Map
ALG3



General Information
Gene Symbol:   
ALG3
Protein name:   
Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase
Enzyme Class:   
Glycosyltransferase
CAZy Family:   
GT58
E.C. No:   
2.4.1.258
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
• Alg 3 is the first enzyme that acts on the lumen-oriented LLO. It adds α1,3-linked mannose to the α1,6 mannose arm. The enzyme uses dolichylphosphomannose (Dol-P-Man) as a donor and Man5GlcNAc2-PP-Dol as an acceptor substrate
• Mutations in Alg 3 results in CDG-Id

Related Pathway
KEGG ORTHOLOGY:   
K03845
KEGG Pathway:   
ko00510  ko00513  ko01100 
Reactome:   
R-HSA-446193
Related Database
Organism:   
Homo sapiens
Uniprot:   
Q92685 
NCBI GeneID:   
10195
GlyMap GeneID:   
10195
DNA aRefSeq:   
NM_001006941.2 
Protein RefSeq:   
NP_001006942.1 
BRENDA:   
Kinetic info.
OMIM number:   
608750
GeneCards database:   
ALG3
Enzyme Specificity
Glycan Type:  
     N-linked
Compartment:  
     ER
Substrate:  
     Man(a1-6)...GlcNAc(b1-4)GlcNAc(a1-?)Dol-PP
Product:  
     Man(a1-3)Man(a1-6)...GlcNAc(b1-4)GlcNAc(a1-?)Dol-PP
Constraints:  
     nMan=5&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 160 140 120 100 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-3202 63-70 -0.713 99.0 -0.701 99.0 noncon
hsa-miR-3117-3p 183-190 -0.644 99.0 -0.042 53.0 noncon
hsa-miR-2682-3p 189-196 -0.641 99.0 -0.042 68.0 noncon
hsa-miR-3169 182-189 -0.632 99.0 -0.041 67.0 noncon
hsa-miR-6781-3p 189-196 -0.604 99.0 -0.04 69.0 noncon
hsa-miR-519d-3p 194-201 -0.588 99.0 -0.039 84.0 con
hsa-miR-20b-5p 194-201 -0.58 99.0 -0.038 85.0 con
hsa-miR-17-5p 194-201 -0.572 99.0 -0.038 84.0 con
hsa-miR-106a-5p 194-201 -0.569 99.0 -0.038 84.0 con
hsa-miR-93-5p 194-201 -0.564 99.0 -0.038 85.0 con
hsa-miR-20a-5p 194-201 -0.559 99.0 -0.037 84.0 con
hsa-miR-106b-5p 194-201 -0.551 99.0 -0.037 84.0 con
hsa-miR-8058 84-91 -0.533 99.0 -0.195 93.0 noncon
hsa-miR-5009-5p 84-91 -0.52 99.0 -0.191 92.0 noncon
hsa-miR-1288-3p 181-187 -0.504 99.0 -0.034 62.0 noncon
hsa-miR-526b-3p 194-201 -0.499 99.0 -0.034 89.0 con
hsa-miR-4686 159-166 -0.497 99.0 -0.183 92.0 noncon
hsa-miR-544b 34-41 -0.451 99.0 -0.451 99.0 noncon
hsa-miR-6774-3p 147-153 -0.442 94.0 -0.165 74.0 noncon
hsa-miR-519e-3p 192-198 -0.426 98.0 -0.03 53.0 noncon
hsa-miR-544b 15-22 -0.42 99.0 -0.42 99.0 noncon
hsa-miR-33b-3p 192-198 -0.4 98.0 -0.028 54.0 noncon
hsa-miR-374c-3p 81-87 -0.374 98.0 -0.368 98.0 noncon
hsa-miR-515-3p 192-198 -0.352 98.0 -0.025 63.0 noncon
hsa-miR-202-5p 205-211 -0.347 98.0 -0.025 59.0 con
hsa-miR-6735-5p 60-66 -0.346 98.0 -0.341 98.0 noncon
hsa-miR-4436b-3p 60-66 -0.346 98.0 -0.341 98.0 noncon
hsa-miR-3657 146-152 -0.34 95.0 -0.13 82.0 noncon
hsa-miR-6879-5p 60-66 -0.324 97.0 -0.319 98.0 noncon
hsa-miR-6828-3p 158-164 -0.316 97.0 -0.121 88.0 noncon
hsa-miR-1273e 177-183 -0.303 97.0 -0.116 84.0 noncon
hsa-miR-4759 183-189 -0.301 97.0 -0.022 43.0 noncon
hsa-miR-7843-5p 60-66 -0.298 98.0 -0.294 98.0 noncon
hsa-miR-4765 173-179 -0.289 97.0 -0.111 88.0 noncon
hsa-miR-4452 169-175 -0.287 98.0 -0.111 93.0 noncon
hsa-miR-571 88-94 -0.283 93.0 -0.109 77.0 noncon
hsa-miR-4632-5p 60-66 -0.276 98.0 -0.272 98.0 noncon
hsa-miR-4313 115-121 -0.273 91.0 -0.105 73.0 noncon
hsa-miR-451b 78-84 -0.269 97.0 -0.265 98.0 noncon
hsa-miR-4766-3p 79-85 -0.262 96.0 -0.258 97.0 noncon
hsa-miR-1911-3p 128-134 -0.26 93.0 -0.101 82.0 noncon
hsa-miR-6790-5p 174-180 -0.257 97.0 -0.1 90.0 noncon
hsa-miR-4529-3p 85-91 -0.257 91.0 -0.1 75.0 noncon
hsa-miR-8083 183-189 -0.251 95.0 -0.018 54.0 noncon