KEGG   PATHWAY: pcad04142
Entry
pcad04142                   Pathway                                
Name
Lysosome - Physeter macrocephalus (sperm whale)
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
pcad04142  Lysosome
pcad04142

Other DBs
GO: 0005764
Organism
Physeter macrocephalus (sperm whale) [GN:pcad]
Gene
102973529  NAGPA; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase isoform X2 [KO:K01125] [EC:3.1.4.45]
102973583  NAGA; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
102973677  [KO:K01319] [EC:3.4.21.20]
102973706  ARSB; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
102974230  NPC2; NPC intracellular cholesterol transporter 2 [KO:K13443]
102974243  CTSH; pro-cathepsin H isoform X1 [KO:K01366] [EC:3.4.22.16]
102974263  SMPD1; sphingomyelin phosphodiesterase isoform X1 [KO:K12350] [EC:3.1.4.12]
102974290  AP3S2; AP-3 complex subunit sigma-2 isoform X1 [KO:K12399]
102974313  AP3B2; AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
102974434  CLN5; ceroid-lipofuscinosis neuronal protein 5 isoform X1 [KO:K12390]
102974919  DMXL1; dmX-like protein 1 isoform X3 [KO:K24155]
102974923  [KO:K01365] [EC:3.4.22.15]
102975289  ATP6V0A4; V-type proton ATPase 116 kDa subunit a 4 [KO:K02154]
102975403  NAGLU; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
102975673  CTSA; lysosomal protective protein isoform X18 [KO:K13289] [EC:3.4.16.5]
102976000  ATP6V0A1; V-type proton ATPase 116 kDa subunit a 1 isoform X1 [KO:K02154]
102976144  AP4M1; AP-4 complex subunit mu-1 [KO:K12402]
102976155  CTSF; cathepsin F isoform X1 [KO:K01373] [EC:3.4.22.41]
102976611  AP3B1; AP-3 complex subunit beta-1 [KO:K12397]
102976976  HGSNAT; heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
102977037  ASAH1; acid ceramidase isoform X1 [KO:K12348] [EC:3.5.1.23]
102977235  CTSD; cathepsin D [KO:K01379] [EC:3.4.23.5]
102977368  AP3M2; AP-3 complex subunit mu-2 [KO:K12398]
102977382  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
102977386  PPT2; lysosomal thioesterase PPT2 isoform X5 [KO:K01074] [EC:3.1.2.22]
102977428  GGA2; ADP-ribosylation factor-binding protein GGA2 [KO:K12404]
102977484  GNPTAB; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta isoform X1 [KO:K08239] [EC:2.7.8.17]
102977619  ABCA2; ATP-binding cassette sub-family A member 2 [KO:K05642]
102977713  ACP5; tartrate-resistant acid phosphatase type 5 [KO:K14379] [EC:3.1.3.2]
102977744  AP1G1; AP-1 complex subunit gamma-1 [KO:K12391]
102977771  ARSG; arylsulfatase G isoform X2 [KO:K12381] [EC:3.1.6.-]
102977981  CD164; sialomucin core protein 24 isoform X1 [KO:K06546]
102978040  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
102978346  GUSB; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
102978507  GNS; N-acetylglucosamine-6-sulfatase isoform X1 [KO:K01137] [EC:3.1.6.14]
102978552  GAA; lysosomal alpha-glucosidase isoform X2 [KO:K12316] [EC:3.2.1.20]
102978613  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit c [KO:K02155]
102978978  AP1S2; AP-1 complex subunit sigma-2 [KO:K12394]
102979042  CTSW; cathepsin W isoform X4 [KO:K08569] [EC:3.4.22.-]
102979493  TCIRG1; V-type proton ATPase 116 kDa subunit a 3 [KO:K02154]
102979608  GM2A; ganglioside GM2 activator [KO:K12383]
102979609  LAMP3; lysosome-associated membrane glycoprotein 3 isoform X1 [KO:K06562]
102979762  CD63; CD63 antigen [KO:K06497]
102979785  CTSS; cathepsin S isoform X1 [KO:K01368] [EC:3.4.22.27]
102979953  SGSH; N-sulphoglucosamine sulphohydrolase isoform X1 [KO:K01565] [EC:3.10.1.1]
102980049  SCARB2; lysosome membrane protein 2 isoform X1 [KO:K12384]
102980180  NCOA7; nuclear receptor coactivator 7 isoform X1 [KO:K25442]
102980378  CTSK; cathepsin K isoform X1 [KO:K01371] [EC:3.4.22.38]
102980786  M6PR; cation-dependent mannose-6-phosphate receptor [KO:K10089]
102980865  AP3S1; LOW QUALITY PROTEIN: AP-3 complex subunit sigma-1 [KO:K12399]
102980876  ATP6V0D2; V-type proton ATPase subunit d 2 [KO:K02146]
102981075  ENTPD4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X2 [KO:K12305] [EC:3.6.1.6]
102981101  NPC1; NPC intracellular cholesterol transporter 1 isoform X1 [KO:K12385]
102981234  ARSA; arylsulfatase A isoform X2 [KO:K01134] [EC:3.1.6.8]
102981243  GGA3; ADP-ribosylation factor-binding protein GGA3 isoform X5 [KO:K12404]
102981449  ATP6V1H; V-type proton ATPase subunit H isoform X1 [KO:K02144]
102981618  HYAL4; hyaluronidase-4 [KO:K01197] [EC:3.2.1.35]
102981880  FUCA2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
102981903  SPAM1; hyaluronidase PH-20 [KO:K01197] [EC:3.2.1.35]
102981911  GALC; galactocerebrosidase isoform X2 [KO:K01202] [EC:3.2.1.46]
102981971  HEXA; beta-hexosaminidase subunit alpha [KO:K12373] [EC:3.2.1.52]
102982017  DNASE2B; deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
102982063  [KO:K12387]
102982311  IGF2R; cation-independent mannose-6-phosphate receptor [KO:K06564]
102982386  AP1B1; AP-1 complex subunit beta-1 isoform X3 [KO:K12392]
102982591  CLN3; battenin isoform X2 [KO:K12389]
102982666  NAPSA; LOW QUALITY PROTEIN: napsin-A [KO:K08565] [EC:3.4.23.-]
102982928  FUCA1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
102983593  PLA2G15; phospholipase A2 group XV isoform X1 [KO:K06129] [EC:3.1.1.5]
102983735  [KO:K01136] [EC:3.1.6.13]
102983822  CTSB; cathepsin B isoform X1 [KO:K01363] [EC:3.4.22.1]
102983927  IDUA; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
102984345  LIPA; lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
102984870  [KO:K01319] [EC:3.4.21.20]
102985112  CLTB; clathrin light chain B isoform X1 [KO:K04645]
102985260  AP4S1; AP-4 complex subunit sigma-1 [KO:K12403]
102985411  CTNS; cystinosin [KO:K12386]
102985837  [KO:K03661]
102985977  MCOLN1; mucolipin-1 isoform X1 [KO:K04992]
102986254  GBA1; lysosomal acid glucosylceramidase [KO:K01201] [EC:3.2.1.45]
102986289  SLC17A5; sialin isoform X1 [KO:K12301]
102986504  MEAK7; MTOR-associated protein MEAK7 isoform X1 [KO:K27947]
102986918  ATP6V0A2; V-type proton ATPase 116 kDa subunit a 2 isoform X3 [KO:K02154]
102986987  DMXL2; dmX-like protein 2 isoform X1 [KO:K24155]
102987265  CLTC; clathrin heavy chain 1 isoform X1 [KO:K04646]
102987441  MANBA; beta-mannosidase isoform X1 [KO:K01192] [EC:3.2.1.25]
102987538  CD68; macrosialin [KO:K06501]
102987747  SUMF1; formylglycine-generating enzyme isoform X2 [KO:K13444] [EC:1.8.3.7]
102988126  [KO:K12311] [EC:3.2.1.24]
102988275  LAMP2; lysosome-associated membrane glycoprotein 2 isoform X2 [KO:K06528]
102988350  AP3M1; AP-3 complex subunit mu-1 [KO:K12398]
102988497  AP1M2; AP-1 complex subunit mu-2 isoform X1 [KO:K12393]
102988543  [KO:K01365] [EC:3.4.22.15]
102988616  LAPTM5; lysosomal-associated transmembrane protein 5 [KO:K12387]
102988695  AP4B1; AP-4 complex subunit beta-1 [KO:K12401]
102988804  [KO:K01202] [EC:3.2.1.46]
102988812  GGA1; ADP-ribosylation factor-binding protein GGA1 [KO:K12404]
102988893  CLTA; clathrin light chain A isoform X8 [KO:K04644]
102989308  SLC11A2; natural resistance-associated macrophage protein 2 isoform X1 [KO:K21398]
102989315  WDR7; WD repeat-containing protein 7 isoform X3 [KO:K24738]
102989358  AGA; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase isoform X1 [KO:K01444] [EC:3.5.1.26]
102989369  HEXB; beta-hexosaminidase subunit beta isoform X1 [KO:K12373] [EC:3.2.1.52]
102989710  ABCB9; ABC-type oligopeptide transporter ABCB9 [KO:K05656]
102990477  GLA; alpha-galactosidase A isoform X1 [KO:K01189] [EC:3.2.1.22]
102990562  PPT1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
102990710  LAPTM4A; lysosomal-associated transmembrane protein 4A [KO:K12387]
102991374  LITAF; lipopolysaccharide-induced tumor necrosis factor-alpha factor [KO:K19363]
102991400  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit c'' isoform X1 [KO:K03661]
102991458  PSAP; prosaposin [KO:K12382]
102991473  ATP6V0D1; V-type proton ATPase subunit d 1 isoform X1 [KO:K02146]
102991915  GLB1; beta-galactosidase [KO:K12309] [EC:3.2.1.23]
102992342  LAPTM4B; lysosomal-associated transmembrane protein 4B [KO:K12387]
102992611  MFSD8; major facilitator superfamily domain-containing protein 8 isoform X2 [KO:K12307]
102993000  CTSZ; cathepsin Z [KO:K08568] [EC:3.4.18.1]
102993175  SLC11A1; natural resistance-associated macrophage protein 1 isoform X2 [KO:K12347]
102993949  AP4E1; AP-4 complex subunit epsilon-1 isoform X16 [KO:K12400]
102994133  SORT1; sortilin isoform X1 [KO:K12388]
102994327  LGMN; legumain [KO:K01369] [EC:3.4.22.34]
102994340  NEU1; sialidase-1 isoform X1 [KO:K01186] [EC:3.2.1.18]
102994689  AP1M1; AP-1 complex subunit mu-1 [KO:K12393]
102994698  AP3D1; AP-3 complex subunit delta-1 isoform X1 [KO:K12396]
102994956  DNASE2; deoxyribonuclease-2-alpha [KO:K01158] [EC:3.1.22.1]
102995041  TPP1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
102995269  AP1S3; AP-1 complex subunit sigma-3 isoform X1 [KO:K12395]
102995376  CTSO; cathepsin O isoform X1 [KO:K01374] [EC:3.4.22.42]
102995474  HYAL2; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
102995531  AP1S1; AP-1 complex subunit sigma-1A isoform X1 [KO:K12394]
102995899  [KO:K01132] [EC:3.1.6.4]
102995952  GNPTG; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
102996103  [KO:K01197] [EC:3.2.1.35]
102996148  CTSL; procathepsin L isoform X2 [KO:K01365] [EC:3.4.22.15]
102996374  HYAL3; hyaluronidase-3 isoform X1 [KO:K01197] [EC:3.2.1.35]
102996895  ACP2; lysosomal acid phosphatase isoform X1 [KO:K14410] [EC:3.1.3.2]
112063763  PSAPL1; LOW QUALITY PROTEIN: proactivator polypeptide-like 1 [KO:K12382]
112064315  [KO:K01186] [EC:3.2.1.18]
112067373  [KO:K01365] [EC:3.4.22.15]
112067583  CTSE; LOW QUALITY PROTEIN: cathepsin E [KO:K01382] [EC:3.4.23.34]
112067657  [KO:K01319] [EC:3.4.21.20]
114483858  AP1G2; AP-1 complex subunit gamma-like 2 [KO:K12391]
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
pcad00511  Other glycan degradation
pcad00531  Glycosaminoglycan degradation
pcad04130  SNARE interactions in vesicular transport
pcad04140  Autophagy - animal
pcad04144  Endocytosis
KO pathway
ko04142   

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