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
RPN1



General Information
Gene Symbol:   
RPN1
Protein name:   
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
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:   
K12666
KEGG Pathway:   
ko00510  ko00513  ko01100  ko04141 
Reactome:   
R-HSA-1799339
Related Database
Organism:   
Homo sapiens
Uniprot:   
P04843 
NCBI GeneID:   
6184
GlyMap GeneID:   
6184
DNA aRefSeq:   
NM_002950.3 
Protein RefSeq:   
NP_002941.1 
BRENDA:   
Kinetic info.
OMIM number:   
180470
GeneCards database:   
RPN1
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 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-4493 115-122 -0.532 99.0 -0.532 99.0 noncon
hsa-miR-4763-5p 49-56 -0.524 98.0 -0.524 99.0 noncon
hsa-miR-1236-3p 124-131 -0.508 99.0 -0.508 99.0 noncon
hsa-miR-4712-3p 463-470 -0.497 99.0 -0.006 43.0 noncon
hsa-miR-27a-3p 430-437 -0.49 99.0 -0.009 50.0 con
hsa-miR-27b-3p 430-437 -0.49 99.0 -0.009 50.0 con
hsa-miR-296-5p 21-28 -0.48 97.0 -0.48 98.0 noncon
hsa-miR-3929 310-317 -0.467 99.0 -0.45 99.0 noncon
hsa-miR-6805-5p 322-328 -0.453 98.0 -0.437 98.0 noncon
hsa-miR-4419b 310-317 -0.451 99.0 -0.435 99.0 noncon
hsa-miR-6848-5p 321-327 -0.44 96.0 -0.424 96.0 noncon
hsa-miR-4478 310-317 -0.435 99.0 -0.419 99.0 noncon
hsa-miR-4445-3p 161-167 -0.43 97.0 -0.43 98.0 noncon
hsa-miR-6846-5p 321-327 -0.429 96.0 -0.414 96.0 noncon
hsa-miR-6871-5p 221-227 -0.424 99.0 -0.424 99.0 noncon
hsa-miR-4301 67-74 -0.419 99.0 -0.419 99.0 noncon
hsa-miR-3154 337-344 -0.413 99.0 -0.398 99.0 noncon
hsa-miR-548al 161-167 -0.412 97.0 -0.412 98.0 noncon
hsa-miR-8080 169-176 -0.411 99.0 -0.411 99.0 noncon
hsa-miR-5683 104-111 -0.398 99.0 -0.398 99.0 noncon
hsa-miR-6798-5p 323-329 -0.38 98.0 -0.367 98.0 noncon
hsa-miR-377-3p 402-409 -0.379 98.0 -0.36 98.0 noncon
hsa-miR-532-3p 69-75 -0.361 98.0 -0.361 99.0 noncon
hsa-miR-4999-3p 65-71 -0.342 96.0 -0.342 97.0 noncon
hsa-miR-7703 368-374 -0.341 98.0 -0.324 98.0 noncon
hsa-miR-3945 333-339 -0.339 97.0 -0.327 97.0 noncon
hsa-miR-342-3p 364-370 -0.336 98.0 -0.32 98.0 noncon
hsa-miR-589-3p 287-294 -0.325 98.0 -0.314 99.0 noncon
hsa-miR-4506 223-229 -0.318 97.0 -0.318 98.0 noncon
hsa-miR-653-3p 90-97 -0.318 98.0 -0.318 98.0 noncon
hsa-miR-561-3p 207-214 -0.307 99.0 -0.307 99.0 noncon
hsa-miR-421 452-459 -0.305 97.0 -0.004 39.0 noncon
hsa-miR-676-5p 454-461 -0.303 98.0 -0.004 53.0 noncon
hsa-miR-2114-5p 426-432 -0.302 97.0 -0.287 98.0 noncon
hsa-miR-6126 116-123 -0.301 98.0 -0.301 98.0 noncon
hsa-miR-193b-3p 88-94 -0.284 92.0 -0.284 95.0 noncon
hsa-miR-193a-3p 88-94 -0.284 92.0 -0.284 95.0 noncon
hsa-miR-1245b-5p 113-119 -0.283 96.0 -0.283 97.0 noncon
hsa-miR-3142 113-119 -0.273 96.0 -0.273 97.0 noncon
hsa-miR-5581-3p 81-87 -0.264 95.0 -0.264 96.0 noncon
hsa-miR-1295b-3p 313-319 -0.263 91.0 -0.254 94.0 noncon
hsa-miR-4470 159-165 -0.258 96.0 -0.258 97.0 noncon
hsa-miR-3156-3p 68-74 -0.254 94.0 -0.254 96.0 noncon