KEGG   PATHWAY: nnt04142
Entry
nnt04142                    Pathway                                
Name
Lysosome - Nestor notabilis (Kea)
Description
Lysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than 40 hydrolases in an acidic environment (pH of about 5). After synthesis in the ER, lysosomal enzymes are decorated with mannose-6-phosphate residues, which are recognized by mannose-6-phosphate receptors in the trans-Golgi network. They are packaged into clathrin-coated vesicles and are transported to late endosomes. Substances for digestion are acquired by the lysosomes via a series of processes including endocytosis, phagocytosis, and autophagy.
Class
Cellular Processes; Transport and catabolism
Pathway map
nnt04142  Lysosome
nnt04142

Other DBs
GO: 0005764
Organism
Nestor notabilis (Kea) [GN:nnt]
Gene
104398979  LITAF; lipopolysaccharide-induced tumor necrosis factor-alpha factor [KO:K19363]
104399125  CLN5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
104399153  [KO:K24155]
104399409  ATP6V1H; V-type proton ATPase subunit H [KO:K02144]
104399516  NPC1; Niemann-Pick C1 protein [KO:K12385]
104399677  FUCA2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
104399687  ATP6V0A1; V-type proton ATPase 116 kDa subunit a isoform 1 [KO:K02154]
104399758  [KO:K12397]
104399765  CTSD; cathepsin D [KO:K01379] [EC:3.4.23.5]
104400079  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
104400113  TLDC1; TLD domain-containing protein 1 [KO:K27947]
104400290  [KO:K01197] [EC:3.2.1.35]
104400293  AP3M2; AP-3 complex subunit mu-2 [KO:K12398]
104400454  [KO:K04645]
104400473  CTSZ; cathepsin Z [KO:K08568] [EC:3.4.18.1]
104400510  [KO:K01365] [EC:3.4.22.15]
104400575  CTSO; cathepsin O [KO:K01374] [EC:3.4.22.42]
104400670  HEXB; beta-hexosaminidase subunit beta [KO:K12373] [EC:3.2.1.52]
104400760  ATP6V0A2; V-type proton ATPase 116 kDa subunit a isoform 2 [KO:K02154]
104401130  GGA2; ADP-ribosylation factor-binding protein GGA2 [KO:K12404]
104401215  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
104401408  [KO:K12395]
104401671  ATP6V0A4; V-type proton ATPase 116 kDa subunit a isoform 4 [KO:K02154]
104401713  MANBA; beta-mannosidase [KO:K01192] [EC:3.2.1.25]
104401800  AP4E1; AP-4 complex subunit epsilon-1 [KO:K12400]
104401933  [KO:K12381] [EC:3.1.6.-]
104402056  GNPTAB; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
104402198  FUCA1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
104402303  [KO:K01197] [EC:3.2.1.35]
104402632  GALC; galactocerebrosidase [KO:K01202] [EC:3.2.1.46]
104402942  ABCB9; ATP-binding cassette sub-family B member 9 [KO:K05656]
104402954  GGA3; ADP-ribosylation factor-binding protein GGA3 [KO:K12404]
104403155  M6PR; cation-dependent mannose-6-phosphate receptor [KO:K10089]
104403194  LAPTM5; lysosomal-associated transmembrane protein 5 [KO:K12387]
104403400  PLA2G15; group XV phospholipase A2 [KO:K06129] [EC:3.1.1.5]
104403415  [KO:K01382] [EC:3.4.23.34]
104403456  HEXA; beta-hexosaminidase subunit alpha [KO:K12373] [EC:3.2.1.52]
104403722  [KO:K14410] [EC:3.1.3.2]
104403930  GNS; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
104403950  AP3B2; LOW QUALITY PROTEIN: AP-3 complex subunit beta-2 [KO:K12397]
104404039  SUMF1; sulfatase-modifying factor 1 [KO:K13444] [EC:1.8.3.7]
104404140  AP3D1; AP-3 complex subunit delta-1 [KO:K12396]
104404155  ARSB; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
104404185  CLTC; clathrin heavy chain 1 isoform X1 [KO:K04646]
104404301  ARSA; arylsulfatase A [KO:K01134] [EC:3.1.6.8]
104404306  CTSE; cathepsin E [KO:K01382] [EC:3.4.23.34]
104404371  [KO:K12394]
104404615  IDUA; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
104404738  [KO:K06562]
104404949  HGSNAT; heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
104405253  ENTPD4; ectonucleoside triphosphate diphosphohydrolase 4 [KO:K12305] [EC:3.6.1.6]
104405276  CTSH; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
104405462  IDS; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
104405610  CD164; sialomucin core protein 24 [KO:K06546]
104406087  TPP1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
104406147  NCOA7; nuclear receptor coactivator 7 isoform X1 [KO:K25442]
104406197  WDR7; WD repeat-containing protein 7 [KO:K24738]
104406385  [KO:K02146]
104406628  AP1B1; AP-1 complex subunit beta-1 [KO:K12392]
104407369  AP3M1; LOW QUALITY PROTEIN: AP-3 complex subunit mu-1 [KO:K12398]
104407380  GNPTG; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
104407594  [KO:K01197] [EC:3.2.1.35]
104407817  CTNS; cystinosin [KO:K12386]
104407874  NAGA; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
104407957  SLC17A5; sialin [KO:K12301]
104407975  GBA; LOW QUALITY PROTEIN: glucosylceramidase [KO:K01201] [EC:3.2.1.45]
104407977  AP4S1; AP-4 complex subunit sigma-1 [KO:K12403]
104407979  GGA1; ADP-ribosylation factor-binding protein GGA1 isoform X1 [KO:K12404]
104408151  GLB1; beta-galactosidase [KO:K12309] [EC:3.2.1.23]
104408212  [KO:K12316] [EC:3.2.1.20]
104408381  DNASE2B; deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
104408430  CTSC; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
104408606  ASAH1; acid ceramidase [KO:K12348] [EC:3.5.1.23]
104408637  [KO:K12382]
104408638  PSAP; prosaposin [KO:K12382]
104408690  MFSD8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
104408728  [KO:K04646]
104409034  [KO:K04992]
104409341  GALNS; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
104409361  CTSS; cathepsin S isoform X1 [KO:K01368] [EC:3.4.22.27]
104409362  CTSK; cathepsin K [KO:K01371] [EC:3.4.22.38]
104409645  GM2A; ganglioside GM2 activator [KO:K12383]
104409676  ABCA2; LOW QUALITY PROTEIN: ATP-binding cassette sub-family A member 2 [KO:K05642]
104410460  PPT1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
104410571  NPC2; epididymal secretory protein E1 [KO:K13443]
104410826  LAPTM4A; lysosomal-associated transmembrane protein 4A [KO:K12387]
104410959  GLA; alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
104410999  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
104411364  [KO:K01052] [EC:3.1.1.13]
104411679  AGA; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
104411810  DMXL1; dmX-like protein 1 isoform X1 [KO:K24155]
104411908  LGMN; legumain [KO:K01369] [EC:3.4.22.34]
104411923  SLC11A2; natural resistance-associated macrophage protein 2 [KO:K21398]
104411988  AP1M1; AP-1 complex subunit mu-1 [KO:K12393]
104412119  ATP6V0D1; V-type proton ATPase subunit d 1 [KO:K02146]
104412164  NAGPA; LOW QUALITY PROTEIN: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
104412202  LAMP2; lysosome-associated membrane glycoprotein 2 [KO:K06528]
104412501  SLC11A1; natural resistance-associated macrophage protein 1 [KO:K12347]
104412631  CTSB; cathepsin B [KO:K01363] [EC:3.4.22.1]
104412948  SPAM1; LOW QUALITY PROTEIN: hyaluronidase PH-20 [KO:K01197] [EC:3.2.1.35]
104413037  SCARB2; LOW QUALITY PROTEIN: lysosome membrane protein 2 [KO:K12384]
104413466  AP4B1; LOW QUALITY PROTEIN: AP-4 complex subunit beta-1 [KO:K12401]
104413539  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
104413614  [KO:K01052] [EC:3.1.1.13]
104413668  CLTA; clathrin light chain A [KO:K04644]
104413757  IGF2R; LOW QUALITY PROTEIN: cation-independent mannose-6-phosphate receptor [KO:K06564]
Compound
C00002  ATP
C00008  ADP
C00159  D-Mannose
C00275  D-Mannose 6-phosphate
Reference
PMID:12628346
  Authors
Eskelinen EL, Tanaka Y, Saftig P
  Title
At the acidic edge: emerging functions for lysosomal membrane proteins.
  Journal
Trends Cell Biol 13:137-45 (2003)
DOI:10.1016/S0962-8924(03)00005-9
Reference
PMID:1883197
  Authors
Neufeld EF
  Title
Lysosomal storage diseases.
  Journal
Annu Rev Biochem 60:257-80 (1991)
DOI:10.1146/annurev.bi.60.070191.001353
Reference
PMID:2943218
  Authors
von Figura K, Hasilik A
  Title
Lysosomal enzymes and their receptors.
  Journal
Annu Rev Biochem 55:167-93 (1986)
DOI:10.1146/annurev.bi.55.070186.001123
Reference
PMID:15987739
  Authors
Janvier K, Bonifacino JS
  Title
Role of the endocytic machinery in the sorting of lysosome-associated membrane proteins.
  Journal
Mol Biol Cell 16:4231-42 (2005)
DOI:10.1091/mbc.E05-03-0213
Reference
PMID:18635948
  Authors
Vergarajauregui S, Puertollano R
  Title
Mucolipidosis type IV: the importance of functional lysosomes for efficient autophagy.
  Journal
Autophagy 4:832-4 (2008)
DOI:10.4161/auto.6567
Reference
PMID:34249946
  Authors
Jaskolka MC, Winkley SR, Kane PM
  Title
RAVE and Rabconnectin-3 Complexes as Signal Dependent Regulators of Organelle Acidification.
  Journal
Front Cell Dev Biol 9:698190 (2021)
DOI:10.3389/fcell.2021.698190
Reference
PMID:34646033
  Authors
Majdoul S, Compton AA
  Title
Lessons in self-defence: inhibition of virus entry by intrinsic immunity.
  Journal
Nat Rev Immunol 22:339-352 (2022)
DOI:10.1038/s41577-021-00626-8
Related
pathway
nnt00511  Other glycan degradation
nnt00531  Glycosaminoglycan degradation
nnt04130  SNARE interactions in vesicular transport
nnt04140  Autophagy - animal
nnt04144  Endocytosis
KO pathway
ko04142   

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