KEGG   PATHWAY: cpoo04142
Entry
cpoo04142                   Pathway                                
Name
Lysosome - Crocodylus porosus (Australian saltwater crocodile)
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
cpoo04142  Lysosome
cpoo04142

Other DBs
GO: 0005764
Organism
Crocodylus porosus (Australian saltwater crocodile) [GN:cpoo]
Gene
109305553  CTSC; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
109305562  TPP1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
109305570  SMPD1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
109306026  AP1S2; AP-1 complex subunit sigma-2 isoform X1 [KO:K12394]
109306294  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
109306432  CLN5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
109307345  DNASE2B; deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
109307392  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
109307690  HEXB; beta-hexosaminidase subunit beta [KO:K12373] [EC:3.2.1.52]
109307718  WDR7; WD repeat-containing protein 7 isoform X1 [KO:K24738]
109307999  ARSB; arylsulfatase B isoform X1 [KO:K01135] [EC:3.1.6.12]
109308004  AP3B1; AP-3 complex subunit beta-1 isoform X1 [KO:K12397]
109308473  LAMP3; lysosome-associated membrane glycoprotein 3 [KO:K06562]
109308487  [KO:K12307]
109308637  AP1S3; AP-1 complex subunit sigma-3 [KO:K12395]
109308831  AP3B2; AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
109308844  HEXA; beta-hexosaminidase subunit alpha [KO:K12373] [EC:3.2.1.52]
109309022  AP4E1; AP-4 complex subunit epsilon-1 isoform X1 [KO:K12400]
109309028  DMXL2; dmX-like protein 2 isoform X1 [KO:K24155]
109309243  CTSH; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
109309322  MFSD8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
109309427  HGSNAT; heparan-alpha-glucosaminide N-acetyltransferase isoform X1 [KO:K10532] [EC:2.3.1.78]
109309474  SCARB2; lysosome membrane protein 2 [KO:K12384]
109309699  CTSO; cathepsin O isoform X1 [KO:K01374] [EC:3.4.22.42]
109309774  AGA; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
109310182  GM2A; ganglioside GM2 activator [KO:K12383]
109310232  CLTB; clathrin light chain B isoform X1 [KO:K04645]
109310385  PLA2G15; group XV phospholipase A2 [KO:K06129] [EC:3.1.1.5]
109310441  [KO:K13289] [EC:3.4.16.5]
109310667  TLDC1; TLD domain-containing protein 1 isoform X1 [KO:K27947]
109310712  GALNS; N-acetylgalactosamine-6-sulfatase isoform X1 [KO:K01132] [EC:3.1.6.4]
109310755  AP1G1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
109310928  GLA; alpha-galactosidase A isoform X1 [KO:K01189] [EC:3.2.1.22]
109311158  SUMF1; sulfatase-modifying factor 1 isoform X1 [KO:K13444] [EC:1.8.3.7]
109311615  LAPTM4A; lysosomal-associated transmembrane protein 4A isoform X1 [KO:K12387]
109311789  [KO:K12309] [EC:3.2.1.23]
109311800  SLC17A5; sialin [KO:K12301]
109311925  CD164; sialomucin core protein 24 [KO:K06546]
109311993  NCOA7; nuclear receptor coactivator 7 isoform X1 [KO:K25442]
109312056  CTSB; cathepsin B [KO:K01363] [EC:3.4.22.1]
109312382  AP1M1; AP-1 complex subunit mu-1 [KO:K12393]
109312483  PSAP; LOW QUALITY PROTEIN: prosaposin [KO:K12382]
109312484  [KO:K12382]
109312536  [KO:K01052] [EC:3.1.1.13]
109312537  [KO:K01052] [EC:3.1.1.13]
109312697  ABCB9; ATP-binding cassette sub-family B member 9 isoform X1 [KO:K05656]
109312718  ATP6V0A2; V-type proton ATPase 116 kDa subunit a [KO:K02154]
109312799  CLTCL1; clathrin heavy chain 2 isoform X1 [KO:K04646]
109312937  AP1B1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
109313296  CTSA; lysosomal protective protein [KO:K13289] [EC:3.4.16.5]
109313506  LITAF; lipopolysaccharide-induced tumor necrosis factor-alpha factor [KO:K19363]
109313532  NAGPA; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
109313533  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
109313575  LAMP2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
109313625  IDS; iduronate 2-sulfatase isoform X1 [KO:K01136] [EC:3.1.6.13]
109314102  ABCA2; ATP-binding cassette sub-family A member 2 [KO:K05642]
109314594  GGA2; ADP-ribosylation factor-binding protein GGA2 [KO:K12404]
109314734  [KO:K12316] [EC:3.2.1.20]
109314896  SGSH; N-sulphoglucosamine sulphohydrolase isoform X1 [KO:K01565] [EC:3.10.1.1]
109314949  ARSG; arylsulfatase G isoform X1 [KO:K12381] [EC:3.1.6.-]
109315059  GGA3; ADP-ribosylation factor-binding protein GGA3 isoform X1 [KO:K12404]
109315191  GAA; lysosomal alpha-glucosidase [KO:K12316] [EC:3.2.1.20]
109315502  [KO:K01382] [EC:3.4.23.34]
109315540  GNS; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
109315644  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
109315652  [KO:K01197] [EC:3.2.1.35]
109315653  [KO:K01197] [EC:3.2.1.35]
109315654  SPAM1; hyaluronidase PH-20 [KO:K01197] [EC:3.2.1.35]
109316231  M6PR; cation-dependent mannose-6-phosphate receptor [KO:K10089]
109316540  ATP6V0A4; V-type proton ATPase 116 kDa subunit a isoform X1 [KO:K02154]
109316551  GNPTAB; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
109316643  GGA1; ADP-ribosylation factor-binding protein GGA1 [KO:K12404]
109316752  NAGA; alpha-N-acetylgalactosaminidase isoform X1 [KO:K01204] [EC:3.2.1.49]
109317061  GUSB; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
109317174  CLTC; clathrin heavy chain 1 isoform X1 [KO:K04646]
109317206  CTNS; cystinosin [KO:K12386]
109317393  AP3M2; AP-3 complex subunit mu-2 isoform X1 [KO:K12398]
109317552  SORT1; sortilin isoform X1 [KO:K12388]
109317695  CTSE; cathepsin E [KO:K01382] [EC:3.4.23.34]
109317856  AP4B1; AP-4 complex subunit beta-1 [KO:K12401]
109318009  NPC1; Niemann-Pick C1 protein [KO:K12385]
109318223  TCIRG1; V-type proton ATPase 116 kDa subunit a [KO:K02154]
109318255  HYAL3; hyaluronidase-3 [KO:K01197] [EC:3.2.1.35]
109318290  HYAL1; hyaluronidase-1 [KO:K01197] [EC:3.2.1.35]
109318293  HYAL2; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
109318370  PPT1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
109318378  FUCA1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
109318648  LAPTM5; lysosomal-associated transmembrane protein 5 [KO:K12387]
109318685  ATP6V1H; V-type proton ATPase subunit H [KO:K02144]
109318706  CTSZ; cathepsin Z [KO:K08568] [EC:3.4.18.1]
109319539  [KO:K01444] [EC:3.5.1.26]
109320066  IGF2R; cation-independent mannose-6-phosphate receptor [KO:K06564]
109320094  ATP6V0D2; V-type proton ATPase subunit d 2 isoform X1 [KO:K02146]
109320160  FUCA2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
109320368  ATP6V0A1; V-type proton ATPase 116 kDa subunit a isoform X1 [KO:K02154]
109320445  [KO:K01365] [EC:3.4.22.15]
109320466  [KO:K01319] [EC:3.4.21.20]
109320705  LAPTM4B; lysosomal-associated transmembrane protein 4B [KO:K12387]
109320945  AP4S1; AP-4 complex subunit sigma-1 [KO:K12403]
109320951  ACP2; lysosomal acid phosphatase [KO:K14410] [EC:3.1.3.2]
109321190  CTSD; cathepsin D [KO:K01379] [EC:3.4.23.5]
109321476  NPC2; epididymal secretory protein E1 [KO:K13443]
109321658  GALC; galactocerebrosidase isoform X1 [KO:K01202] [EC:3.2.1.46]
109321700  LGMN; legumain [KO:K01369] [EC:3.4.22.34]
109321837  ASAH1; acid ceramidase [KO:K12348] [EC:3.5.1.23]
109322232  MANBA; beta-mannosidase [KO:K01192] [EC:3.2.1.25]
109322443  NAGLU; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
109322504  SLC11A1; natural resistance-associated macrophage protein 1 [KO:K12347]
109323209  [KO:K06497]
109323287  AP3S1; AP-3 complex subunit sigma-1 [KO:K12399]
109323410  IDUA; alpha-L-iduronidase isoform X1 [KO:K01217] [EC:3.2.1.76]
109323420  DMXL1; dmX-like protein 1 isoform X1 [KO:K24155]
109323661  CLTA; clathrin light chain A isoform X1 [KO:K04644]
109323678  [KO:K01365] [EC:3.4.22.15]
109323908  AP3M1; AP-3 complex subunit mu-1 [KO:K12398]
109324008  LIPA; lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
109324285  [KO:K01052] [EC:3.1.1.13]
109324298  [KO:K10532] [EC:2.3.1.78]
109324563  ENTPD4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
109324801  GBA; glucosylceramidase isoform X1 [KO:K01201] [EC:3.2.1.45]
109324822  CTSK; cathepsin K [KO:K01371] [EC:3.4.22.38]
109324918  AP3D1; AP-3 complex subunit delta-1 [KO:K12396]
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
cpoo00511  Other glycan degradation
cpoo00531  Glycosaminoglycan degradation
cpoo04130  SNARE interactions in vesicular transport
cpoo04140  Autophagy - animal
cpoo04144  Endocytosis
KO pathway
ko04142   

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