KEGG   PATHWAY: oro04142
Entry
oro04142                    Pathway                                
Name
Lysosome - Odobenus rosmarus divergens (Pacific walrus)
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
oro04142  Lysosome
oro04142

Other DBs
GO: 0005764
Organism
Odobenus rosmarus divergens (Pacific walrus) [GN:oro]
Gene
101382977  ATP6V0A2; V-type proton ATPase 116 kDa subunit a isoform 2 [KO:K02154]
101374534  ATP6V0A1; V-type proton ATPase 116 kDa subunit a isoform 1 isoform X2 [KO:K02154]
101381351  ATP6V0A4; V-type proton ATPase 116 kDa subunit a isoform 4 [KO:K02154]
101376099  TCIRG1; V-type proton ATPase 116 kDa subunit a isoform 3 [KO:K02154]
101363374  ATP6V0D1; V-type proton ATPase subunit d 1 [KO:K02146]
101374455  ATP6V0D2; V-type proton ATPase subunit d 2 [KO:K02146]
101375398  ATP6V1H; V-type proton ATPase subunit H isoform X1 [KO:K02144]
101382296  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
101382467  V-type proton ATPase 16 kDa proteolipid subunit-like [KO:K02155]
101377607  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
101365399  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit isoform X1 [KO:K03661]
101386924  DMXL1; dmX-like protein 1 isoform X1 [KO:K24155]
101383842  DMXL2; dmX-like protein 2 isoform X1 [KO:K24155]
101383026  WDR7; WD repeat-containing protein 7 isoform X1 [KO:K24738]
101376439  NCOA7; nuclear receptor coactivator 7 isoform X2 [KO:K25442]
101379146  CTSA; lysosomal protective protein [KO:K13289] [EC:3.4.16.5]
101375531  CTSB; cathepsin B [KO:K01363] [EC:3.4.22.1]
101371731  CTSC; dipeptidyl peptidase 1 isoform X1 [KO:K01275] [EC:3.4.14.1]
101381080  CTSD; cathepsin D isoform X1 [KO:K01379] [EC:3.4.23.5]
101364641  CTSE; cathepsin E isoform X1 [KO:K01382] [EC:3.4.23.34]
101365457  CTSF; cathepsin F [KO:K01373] [EC:3.4.22.41]
101383583  CTSG; cathepsin G [KO:K01319] [EC:3.4.21.20]
101362840  CTSH; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
101371209  CTSK; cathepsin K [KO:K01371] [EC:3.4.22.38]
101362126  cathepsin L1 [KO:K01365] [EC:3.4.22.15]
101364724  cathepsin L1-like [KO:K01365] [EC:3.4.22.15]
101382346  cathepsin L1-like [KO:K01365] [EC:3.4.22.15]
101364428  cathepsin L1-like [KO:K01365] [EC:3.4.22.15]
101379477  CTSO; cathepsin O [KO:K01374] [EC:3.4.22.42]
101370623  CTSS; cathepsin S isoform X2 [KO:K01368] [EC:3.4.22.27]
101377645  CTSW; cathepsin W [KO:K08569] [EC:3.4.22.-]
101365974  CTSZ; cathepsin Z [KO:K08568] [EC:3.4.18.1]
101369553  NAPSA; napsin-A [KO:K08565] [EC:3.4.23.-]
101384948  LGMN; legumain [KO:K01369] [EC:3.4.22.34]
101364552  TPP1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
101367352  GLA; alpha-galactosidase A isoform X1 [KO:K01189] [EC:3.2.1.22]
101367677  GLB1; beta-galactosidase [KO:K12309] [EC:3.2.1.23]
101386503  GAA; lysosomal alpha-glucosidase isoform X1 [KO:K12316] [EC:3.2.1.20]
101366488  GBA; glucosylceramidase isoform X1 [KO:K01201] [EC:3.2.1.45]
101385570  IDUA; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
101381151  NAGA; alpha-N-acetylgalactosaminidase isoform X2 [KO:K01204] [EC:3.2.1.49]
101375207  NAGLU; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
101363316  GALC; galactocerebrosidase isoform X1 [KO:K01202] [EC:3.2.1.46]
101365214  GUSB; beta-glucuronidase isoform X1 [KO:K01195] [EC:3.2.1.31]
101365465  FUCA1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
101362419  FUCA2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
101380281  HEXA; beta-hexosaminidase subunit alpha isoform X1 [KO:K12373] [EC:3.2.1.52]
101372553  HEXB; beta-hexosaminidase subunit beta [KO:K12373] [EC:3.2.1.52]
101371988  MANBA; beta-mannosidase [KO:K01192] [EC:3.2.1.25]
101367441  MAN2B1; lysosomal alpha-mannosidase isoform X1 [KO:K12311] [EC:3.2.1.24]
101376694  NEU1; sialidase-1 [KO:K01186] [EC:3.2.1.18]
101369009  HYAL3; hyaluronidase-3 isoform X1 [KO:K01197] [EC:3.2.1.35]
101364702  hyaluronidase-4 [KO:K01197] [EC:3.2.1.35]
101365006  SPAM1; hyaluronidase PH-20 [KO:K01197] [EC:3.2.1.35]
101366496  hyaluronidase-1-like [KO:K01197] [EC:3.2.1.35]
101369610  HYAL1; hyaluronidase-1 [KO:K01197] [EC:3.2.1.35]
101370114  HYAL2; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
101377712  ARSA; arylsulfatase A [KO:K01134] [EC:3.1.6.8]
101374250  ARSB; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
101364516  ARSG; arylsulfatase G [KO:K12381] [EC:3.1.6.-]
101366420  GALNS; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
101363282  GNS; N-acetylglucosamine-6-sulfatase isoform X1 [KO:K01137] [EC:3.1.6.14]
101382674  IDS; iduronate 2-sulfatase isoform X1 [KO:K01136] [EC:3.1.6.13]
101385912  SGSH; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
101386245  LIPA; lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
101377914  PLA2G15; group XV phospholipase A2 [KO:K06129] [EC:3.1.1.5]
101365858  DNASE2B; deoxyribonuclease-2-beta isoform X1 [KO:K01158] [EC:3.1.22.1]
101372958  DNASE2; deoxyribonuclease-2-alpha [KO:K01158] [EC:3.1.22.1]
101377768  ACP2; lysosomal acid phosphatase isoform X1 [KO:K14410] [EC:3.1.3.2]
101365788  ACP5; tartrate-resistant acid phosphatase type 5 [KO:K14379] [EC:3.1.3.2]
101383347  SMPD1; sphingomyelin phosphodiesterase isoform X1 [KO:K12350] [EC:3.1.4.12]
101384361  ASAH1; acid ceramidase [KO:K12348] [EC:3.5.1.23]
101373841  AGA; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase isoform X1 [KO:K01444] [EC:3.5.1.26]
101370373  PSAP; prosaposin isoform X1 [KO:K12382]
101382044  GM2A; LOW QUALITY PROTEIN: ganglioside GM2 activator [KO:K12383]
101368745  palmitoyl-protein thioesterase 1-like [KO:K01074] [EC:3.1.2.22]
101362292  PPT2; lysosomal thioesterase PPT2 [KO:K01074] [EC:3.1.2.22]
101386758  PPT1; palmitoyl-protein thioesterase 1 isoform X1 [KO:K01074] [EC:3.1.2.22]
101367700  LAMP1; lysosome-associated membrane glycoprotein 1 isoform X1 [KO:K06528]
101377327  LAMP2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
101385920  LAMP3; lysosome-associated membrane glycoprotein 3 [KO:K06562]
101364491  CD68; macrosialin [KO:K06501]
101379139  CD63; CD63 antigen isoform X2 [KO:K06497]
101378367  SCARB2; lysosome membrane protein 2 isoform X1 [KO:K12384]
101383529  NPC1; LOW QUALITY PROTEIN: Niemann-Pick C1 protein [KO:K12385]
101372072  NPC2; epididymal secretory protein E1 [KO:K13443]
101386268  CTNS; cystinosin isoform X2 [KO:K12386]
101376385  SLC17A5; LOW QUALITY PROTEIN: sialin [KO:K12301]
101370805  SLC11A1; natural resistance-associated macrophage protein 1 isoform X1 [KO:K12347]
101381263  SLC11A2; natural resistance-associated macrophage protein 2 isoform X1 [KO:K21398]
101374324  LAPTM5; lysosomal-associated transmembrane protein 5 isoform X2 [KO:K12387]
101379439  LAPTM4A; lysosomal-associated transmembrane protein 4A [KO:K12387]
101370030  LAPTM4B; LOW QUALITY PROTEIN: lysosomal-associated transmembrane protein 4B [KO:K12387]
101373967  ABCA2; ATP-binding cassette sub-family A member 2 [KO:K05642]
101377562  ABCB9; ATP-binding cassette sub-family B member 9 isoform X1 [KO:K05656]
101379243  CD164; sialomucin core protein 24 [KO:K06546]
101363814  ENTPD4; ectonucleoside triphosphate diphosphohydrolase 4 [KO:K12305] [EC:3.6.1.6]
101369752  SORT1; sortilin isoform X2 [KO:K12388]
101379492  CLN3; battenin isoform X1 [KO:K12389]
101376758  CLN5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
101365354  MFSD8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
101370676  HGSNAT; heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
101368042  SUMF1; sulfatase-modifying factor 1 isoform X1 [KO:K13444] [EC:1.8.3.7]
101376907  GNPTAB; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
101385509  GNPTG; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
101373357  NAGPA; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase isoform X1 [KO:K01125] [EC:3.1.4.45]
101381369  IGF2R; cation-independent mannose-6-phosphate receptor [KO:K06564]
101373474  M6PR; cation-dependent mannose-6-phosphate receptor [KO:K10089]
101364436  CLTA; clathrin light chain A isoform X1 [KO:K04644]
101381905  clathrin light chain A-like isoform X1 [KO:K04644]
101385198  CLTB; clathrin light chain B isoform X1 [KO:K04645]
101362520  CLTC; clathrin heavy chain 1 isoform X3 [KO:K04646]
101383357  CLTCL1; clathrin heavy chain 2 [KO:K04646]
101384511  AP1G2; AP-1 complex subunit gamma-like 2 isoform X1 [KO:K12391]
101362976  AP1G1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
101380679  AP1B1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
101383489  AP1M1; AP-1 complex subunit mu-1 isoform X1 [KO:K12393]
101379506  AP1M2; AP-1 complex subunit mu-2 isoform X2 [KO:K12393]
101382714  AP1S1; AP-1 complex subunit sigma-1A [KO:K12394]
101363008  AP1S2; AP-1 complex subunit sigma-2 [KO:K12394]
101366143  AP-1 complex subunit sigma-2-like [KO:K12394]
101363248  AP1S3; AP-1 complex subunit sigma-3 [KO:K12395]
101367906  AP3D1; AP-3 complex subunit delta-1 isoform X1 [KO:K12396]
101366001  AP3B2; AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
101375402  AP3B1; AP-3 complex subunit beta-1 isoform X1 [KO:K12397]
101376018  AP3M2; AP-3 complex subunit mu-2 [KO:K12398]
101370531  AP3M1; AP-3 complex subunit mu-1 [KO:K12398]
101379812  AP3S1; AP-3 complex subunit sigma-1 isoform X1 [KO:K12399]
101376791  AP-3 complex subunit sigma-2 [KO:K12399]
101382112  AP4E1; AP-4 complex subunit epsilon-1 [KO:K12400]
101366783  AP4B1; AP-4 complex subunit beta-1 isoform X1 [KO:K12401]
101365161  AP4M1; AP-4 complex subunit mu-1 [KO:K12402]
101364683  AP4S1; AP-4 complex subunit sigma-1 [KO:K12403]
101383417  GGA1; ADP-ribosylation factor-binding protein GGA1 isoform X2 [KO:K12404]
101363677  GGA3; ADP-ribosylation factor-binding protein GGA3 isoform X1 [KO:K12404]
101383376  GGA2; ADP-ribosylation factor-binding protein GGA2 [KO:K12404]
101363074  MCOLN1; mucolipin-1 [KO:K04992]
101375855  LITAF; lipopolysaccharide-induced tumor necrosis factor-alpha factor [KO:K19363]
101380392  lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
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 10.1038/s41577-021-00626-8 (2021)
DOI:10.1038/s41577-021-00626-8
Related
pathway
oro00511  Other glycan degradation
oro00531  Glycosaminoglycan degradation
oro04130  SNARE interactions in vesicular transport
oro04140  Autophagy - animal
oro04144  Endocytosis
KO pathway
ko04142   
LinkDB

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