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
RPN2



General Information
Gene Symbol:   
RPN2
Protein name:   
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
Enzyme Class:   
CAZy Family:   
E.C. No:   
Organs:   
Reaction (SNFG):   

No reaction →
Reaction (IUBMB):   
No specified reaction.
About

• A multi-membrane protein ER membrane associated protein complex that mediates the en-bloc transfer of 14 sugar LLO to N-X-S/T motif in nascent polypeptide
• STT3 is the catalytic core of this complex
• Stt3 forms a complex with the accessory membrane proteins DDOST/OST48, RPN1/ribophorin I, RPN2/ribophorin II, DAD1, Ost4, TUSC3/N33 and MGAT1/IAP in mammals for maximal ativity.
• There are two STT3 genes: STT3A and STT3B. Human Stt3A and Stt3B have redundant functions in the co-translational N-glycosylation. Stt3B also mediates the post-translational N-glycosylation after some time, rather than just at the time when the protein enters the ER from the ribosome.
• Glc[0-3]Man[0-9]GlcNAc2β1-PP-Dol + Asn-Xaa-Ser/Thr -> Dol-PP + Glc[0-3]Man[0-9]GlcNAc2β1-Asn-Xaa-Ser/Thr.

Related Pathway
KEGG ORTHOLOGY:   
K12667
KEGG Pathway:   
ko00510  ko00513  ko01100  ko04141 
Reactome:   
R-HSA-1799339
Related Database
Organism:   
Homo sapiens
Uniprot:   
P04844 
NCBI GeneID:   
6185
GlyMap GeneID:   
6185
DNA aRefSeq:   
NM_001135771.2 
Protein RefSeq:   
NP_001129243.1 
BRENDA:   
Kinetic info.
OMIM number:   
180490
GeneCards database:   
RPN2
Enzyme Specificity
Glycan Type:  
     N-linked
Compartment:  
     ER
Substrate:  
     No reaction
Product:  
     
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 140 120 100 80 60 40 20 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 800 700 600 500 400 300 200 100 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-7848-3p 288-295 -0.772 99.0 -0.77 99.0 noncon
hsa-miR-378e 114-121 -0.732 99.0 -0.732 99.0 noncon
hsa-miR-422a 114-121 -0.732 99.0 -0.732 99.0 noncon
hsa-miR-378i 114-121 -0.732 99.0 -0.732 99.0 noncon
hsa-miR-378h 114-121 -0.732 99.0 -0.732 99.0 noncon
hsa-miR-378d 114-121 -0.732 99.0 -0.732 99.0 noncon
hsa-miR-378c 114-121 -0.732 99.0 -0.732 99.0 noncon
hsa-miR-378a-3p 114-121 -0.732 99.0 -0.732 99.0 noncon
hsa-miR-378b 114-121 -0.708 99.0 -0.708 99.0 noncon
hsa-miR-378f 114-121 -0.708 99.0 -0.708 99.0 noncon
hsa-miR-6861-5p 236-243 -0.688 99.0 -0.686 99.0 noncon
hsa-miR-555 234-241 -0.611 99.0 -0.609 99.0 noncon
hsa-let-7d-5p 1347-1354 -0.578 99.0 0.0 12.0 noncon
hsa-miR-98-5p 1347-1354 -0.568 99.0 0.0 13.0 noncon
hsa-let-7g-5p 1347-1354 -0.568 99.0 0.0 13.0 noncon
hsa-miR-4500 1347-1354 -0.568 99.0 0.0 14.0 noncon
hsa-let-7i-5p 1347-1354 -0.568 99.0 0.0 13.0 noncon
hsa-let-7a-5p 1347-1354 -0.56 99.0 0.0 13.0 noncon
hsa-let-7c-5p 1347-1354 -0.56 99.0 0.0 13.0 noncon
hsa-let-7b-5p 1347-1354 -0.56 99.0 0.0 13.0 noncon
hsa-let-7e-5p 1347-1354 -0.56 99.0 0.0 13.0 noncon
hsa-miR-4458 1347-1354 -0.554 99.0 0.0 12.0 noncon
hsa-let-7f-5p 1347-1354 -0.552 99.0 0.0 13.0 noncon
hsa-miR-219a-2-3p 56-63 -0.545 99.0 -0.545 99.0 con
hsa-miR-4733-3p 173-180 -0.521 99.0 -0.52 99.0 noncon
hsa-miR-4659a-3p 71-78 -0.51 99.0 -0.51 99.0 noncon
hsa-miR-4659b-3p 71-78 -0.51 99.0 -0.51 99.0 noncon
hsa-miR-2110 152-159 -0.477 99.0 -0.476 99.0 noncon
hsa-miR-196a-5p 1342-1349 -0.467 98.0 0.0 15.0 noncon
hsa-miR-466 265-272 -0.463 99.0 -0.462 99.0 noncon
hsa-miR-4677-5p 52-59 -0.46 99.0 -0.46 99.0 noncon
hsa-miR-3657 1076-1083 -0.455 98.0 0.0 16.0 noncon
hsa-miR-196b-5p 1342-1349 -0.443 98.0 0.0 15.0 noncon
hsa-miR-3670 178-185 -0.44 98.0 -0.439 99.0 noncon
hsa-miR-31-3p 1208-1215 -0.434 98.0 0.0 22.0 noncon
hsa-miR-561-3p 91-98 -0.433 99.0 -0.433 99.0 noncon
hsa-miR-4686 165-172 -0.413 98.0 -0.412 99.0 noncon
hsa-miR-4650-5p 308-315 -0.412 99.0 0.0 25.0 noncon
hsa-miR-4328 26-33 -0.404 99.0 -0.404 99.0 noncon
hsa-miR-5008-3p 1187-1194 -0.402 98.0 0.0 25.0 noncon
hsa-miR-4788 759-766 -0.38 94.0 0.0 3.0 noncon
hsa-miR-7157-3p 1187-1194 -0.373 98.0 0.0 23.0 noncon
hsa-miR-6737-3p 1187-1194 -0.373 98.0 0.0 23.0 noncon
hsa-miR-4780 1072-1079 -0.373 98.0 0.0 11.0 noncon
hsa-miR-4693-5p 62-68 -0.372 98.0 -0.372 98.0 noncon
hsa-miR-8058 113-119 -0.371 97.0 -0.371 98.0 noncon
hsa-miR-149-5p 1000-1007 -0.368 98.0 0.0 34.0 noncon
hsa-miR-5009-5p 113-119 -0.352 97.0 -0.352 98.0 noncon
hsa-miR-1258 228-234 -0.349 95.0 -0.348 96.0 noncon
hsa-miR-3200-5p 182-189 -0.349 99.0 -0.348 99.0 noncon
hsa-miR-6805-5p 1146-1152 -0.344 93.0 0.0 11.0 noncon
hsa-miR-4672 206-213 -0.341 98.0 -0.34 99.0 noncon
hsa-miR-3907 501-508 -0.339 95.0 0.0 16.0 noncon
hsa-miR-4638-3p 115-121 -0.337 96.0 -0.337 97.0 noncon
hsa-miR-1254 1239-1246 -0.33 98.0 0.0 11.0 noncon
hsa-miR-3116 1239-1246 -0.328 98.0 0.0 15.0 noncon
hsa-miR-1298-3p 238-244 -0.314 96.0 -0.313 97.0 noncon
hsa-miR-760 998-1005 -0.311 94.0 0.0 17.0 noncon
hsa-miR-4688 432-438 -0.306 95.0 0.0 5.0 noncon
hsa-miR-4303 181-187 -0.304 97.0 -0.303 98.0 noncon
hsa-miR-892a 62-68 -0.299 97.0 -0.299 98.0 noncon
hsa-miR-450a-2-3p 153-159 -0.294 93.0 -0.294 95.0 noncon
hsa-miR-548f-5p 133-139 -0.291 99.0 -0.291 99.0 noncon
hsa-miR-6718-5p 1102-1108 -0.285 96.0 0.0 25.0 noncon
hsa-miR-6739-3p 53-59 -0.282 96.0 -0.282 97.0 noncon
hsa-miR-1179 1371-1377 -0.275 97.0 0.0 36.0 noncon
hsa-miR-4275 269-275 -0.274 98.0 -0.273 98.0 noncon
hsa-miR-103a-2-5p 212-218 -0.273 96.0 -0.272 97.0 noncon
hsa-miR-548g-5p 133-139 -0.269 98.0 -0.269 99.0 noncon
hsa-miR-548aj-5p 133-139 -0.269 98.0 -0.269 99.0 noncon
hsa-miR-548x-5p 133-139 -0.269 98.0 -0.269 99.0 noncon
hsa-miR-1257 59-65 -0.268 96.0 -0.268 97.0 noncon
hsa-miR-6891-5p 1308-1314 -0.267 96.0 0.0 26.0 noncon
hsa-miR-3675-5p 543-549 -0.266 92.0 0.0 16.0 noncon
hsa-miR-4318 62-68 -0.265 96.0 -0.265 97.0 noncon
hsa-miR-874-5p 736-743 -0.264 90.0 0.0 5.0 noncon
hsa-miR-203b-5p 1102-1108 -0.263 94.0 0.0 26.0 noncon
hsa-miR-6763-5p 153-159 -0.261 93.0 -0.261 95.0 noncon
hsa-miR-6817-3p 1191-1198 -0.261 97.0 0.0 26.0 noncon
hsa-miR-6733-3p 202-208 -0.26 95.0 -0.259 97.0 noncon
hsa-miR-6071 164-170 -0.26 95.0 -0.26 96.0 noncon
hsa-miR-1270 1012-1019 -0.259 97.0 0.0 27.0 noncon
hsa-miR-6511a-3p 175-181 -0.253 93.0 -0.253 95.0 noncon
hsa-miR-6511b-3p 175-181 -0.253 93.0 -0.253 95.0 noncon
hsa-miR-196a-3p 1254-1261 -0.251 91.0 0.0 8.0 noncon