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
PMM2



General Information
Gene Symbol:   
PMM2
Protein name:   
Phosphomannomutase 2
Enzyme Class:   
CAZy Family:   
E.C. No:   
5.4.2.8
Organs:   
Reaction (SNFG):   

Man(1P) or Man(6P) → Man(6P) or Man(1P)
Reaction (IUBMB):   
No specified reaction.
About

• Phosphomannomutase 1 transfers a phosphate group from the 1 carbon to the 6 carbon on mannose 1 phosphate.
• PMM1 and 2 share 65% homology.
• PMM2 deficiency is recognized as a congenital disease of glycosylation. The lack of available phosphorylated mannose decreases due to the lack of activity and causes underglycosylation. The disease causes a wide array of deformities and metabolic disorders.

Related Pathway
KEGG ORTHOLOGY:   
KEGG Pathway:   
No Record 
Reactome:   
R-HSA-4043911
Related Database
Organism:   
Homo sapiens
Uniprot:   
O15305 
NCBI GeneID:   
5373
GlyMap GeneID:   
5373
DNA aRefSeq:   
NM_000303.2 
Protein RefSeq:   
NP_000294.1 
BRENDA:   
Kinetic info.
OMIM number:   
601785
GeneCards database:   
PMM2
Enzyme Specificity
Glycan Type:  
     
Compartment:  
     
Substrate:  
     Man(1P) or Man(6P)
Product:  
     Man(6P) or Man(1P)
Constraints:  
     None
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 30 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 100 80 60 40 20 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
ENST00000268261 ENST00000565221 ENST00000566540 ENST00000567697 ASCL1
miRNA-GlycoEnzyme Interactome {ref. 9}
PMM2/hsa-miR-6766-5p
miRNA Target Site Type Pos. Context Score Frac. Wt. Context Frac. Conserved Quality
5'... CACAAAAGGUCUUC CCCACCCA ...
3'   GAGUUAUUCUAGACGA GGGUGGG C
 8mer 234-241 -0.405 97.0 -0.405 97.0 noncon
5'... CCCCUAGUCUAAUA CCCACCC U...
3'   GAGUUAUUCUAGACGA GGGUGGG C
 7mer-m8 264-270 -0.356 95.0 -0.356 96.0 noncon
5'... AAAGGUCUUCCCCA CCCACCC C...
3'   GAGUUAUUCUAGACGA GGGUGGG C
 7mer-m8 238-244 -0.236 84.0 -0.236 88.0 noncon
5'... CCCACACGUGCUCA CCCACCC G...
3'   GAGUUAUUCUAGACGA GGGUGGG C
 7mer-m8 89-95 -0.195 76.0 -0.195 82.0 noncon