KEGG   PATHWAY: apla04142
Entry
apla04142                   Pathway                                
Name
Lysosome - Anas platyrhynchos (mallard)
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
apla04142  Lysosome
apla04142

Other DBs
GO: 0005764
Organism
Anas platyrhynchos (mallard) [GN:apla]
Gene
101789387  CTSE; cathepsin E [KO:K01382] [EC:3.4.23.34]
101789467  CTSO; cathepsin O [KO:K01374] [EC:3.4.22.42]
101789511  AP3S2; AP-3 complex subunit sigma-2 isoform X1 [KO:K12399]
101789737  ATP6V1H; V-type proton ATPase subunit H isoform X1 [KO:K02144]
101789835  GGA1; ADP-ribosylation factor-binding protein GGA1 [KO:K12404]
101789967  SCARB2; lysosome membrane protein 2 [KO:K12384]
101790053  AP1G1; AP-1 complex subunit gamma-1 isoform X3 [KO:K12391]
101790373  ACP2; lysosomal acid phosphatase [KO:K14410] [EC:3.1.3.2]
101790487  DMXL1; dmX-like protein 1 isoform X1 [KO:K24155]
101790562  SORT1; sortilin isoform X1 [KO:K12388]
101790763  AP3M2; AP-3 complex subunit mu-2 [KO:K12398]
101790870  AP3D1; LOW QUALITY PROTEIN: AP-3 complex subunit delta-1 [KO:K12396]
101790911  AP1S2; AP-1 complex subunit sigma-2 isoform X1 [KO:K12394]
101791556  DMXL2; dmX-like protein 2 isoform X1 [KO:K24155]
101791839  AP3B2; AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
101792144  FUCA2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
101792345  TPP1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
101792371  ABCB9; ATP-binding cassette sub-family B member 9 isoform X1 [KO:K05656]
101792400  GNPTAB; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta isoform X1 [KO:K08239] [EC:2.7.8.17]
101792449  CTSD; cathepsin D [KO:K01379] [EC:3.4.23.5]
101792450  [KO:K13444] [EC:1.8.3.7]
101792497  NAGA; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
101792515  IDUA; alpha-L-iduronidase isoform X1 [KO:K01217] [EC:3.2.1.76]
101792596  GALNS; N-acetylgalactosamine-6-sulfatase isoform X2 [KO:K01132] [EC:3.1.6.4]
101792648  DNASE2B; deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
101792945  HEXB; beta-hexosaminidase subunit beta [KO:K12373] [EC:3.2.1.52]
101793169  LAMP3; lysosome-associated membrane glycoprotein 3 [KO:K06562]
101793313  [KO:K01052] [EC:3.1.1.13]
101793510  GUSB; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
101793712  AP4E1; AP-4 complex subunit epsilon-1 isoform X2 [KO:K12400]
101793731  CLTA; clathrin light chain A isoform X1 [KO:K04644]
101793816  M6PR; cation-dependent mannose-6-phosphate receptor [KO:K10089]
101794039  SLC17A5; LOW QUALITY PROTEIN: sialin [KO:K12301]
101794155  CTSK; cathepsin K isoform X3 [KO:K01371] [EC:3.4.22.38]
101794268  CTSB; cathepsin B [KO:K01363] [EC:3.4.22.1]
101794415  CLTC; clathrin heavy chain 1 isoform X1 [KO:K04646]
101794564  CTSS; cathepsin S isoform X2 [KO:K01368] [EC:3.4.22.27]
101794741  GGA2; ADP-ribosylation factor-binding protein GGA2 [KO:K12404]
101794974  CLN5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
101795078  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
101795108  LIPA; lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
101795466  LAMP2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
101795480  AP1S3; AP-1 complex subunit sigma-3 [KO:K12395]
101795606  AP1B1; LOW QUALITY PROTEIN: AP-1 complex subunit beta-1 [KO:K12392]
101795708  IGF2R; LOW QUALITY PROTEIN: cation-independent mannose-6-phosphate receptor [KO:K06564]
101795794  HYAL1; hyaluronidase-1 [KO:K01197] [EC:3.2.1.35]
101795828  ARSA; arylsulfatase A [KO:K01134] [EC:3.1.6.8]
101796033  AP3S1; AP-3 complex subunit sigma-1 isoform X1 [KO:K12399]
101796039  AP4S1; AP-4 complex subunit sigma-1 [KO:K12403]
101796060  LAPTM4B; lysosomal-associated transmembrane protein 4B [KO:K12387]
101796293  MFSD8; major facilitator superfamily domain-containing protein 8 isoform X1 [KO:K12307]
101796301  GALC; galactocerebrosidase isoform X1 [KO:K01202] [EC:3.2.1.46]
101796321  PLA2G15; phospholipase A2 group XV isoform X1 [KO:K06129] [EC:3.1.1.5]
101796401  [KO:K12382]
101796667  AP4B1; AP-4 complex subunit beta-1 isoform X1 [KO:K12401]
101796827  AGA; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase isoform X1 [KO:K01444] [EC:3.5.1.26]
101796974  GGA3; ADP-ribosylation factor-binding protein GGA3 [KO:K12404]
101797303  CLTCL1; clathrin heavy chain 2 isoform X1 [KO:K04646]
101797387  AP1M1; AP-1 complex subunit mu-1 [KO:K12393]
101797465  GLB1; beta-galactosidase isoform X1 [KO:K12309] [EC:3.2.1.23]
101797534  ATP6V0A4; V-type proton ATPase 116 kDa subunit a [KO:K02154]
101797539  CTNS; cystinosin [KO:K12386]
101797644  HEXA; beta-hexosaminidase subunit alpha [KO:K12373] [EC:3.2.1.52]
101797831  LAPTM4A; lysosomal-associated transmembrane protein 4A [KO:K12387]
101798454  NPC2; NPC intracellular cholesterol transporter 2 [KO:K13443]
101798677  GNPTG; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
101798729  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
101798773  TCIRG1; V-type proton ATPase 116 kDa subunit a3 [KO:K02154]
101798941  HGSNAT; heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
101799098  [KO:K01197] [EC:3.2.1.35]
101799286  HYAL4; LOW QUALITY PROTEIN: hyaluronidase-4 [KO:K01197] [EC:3.2.1.35]
101799483  ATP6V0A2; LOW QUALITY PROTEIN: V-type proton ATPase 116 kDa subunit a2 [KO:K02154]
101800183  HYAL2; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
101800838  LITAF; lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1 [KO:K19363]
101800840  GLA; LOW QUALITY PROTEIN: alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
101800891  ARSG; arylsulfatase G isoform X1 [KO:K12381] [EC:3.1.6.-]
101800969  NAGPA; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
101801002  ABCA2; ATP-binding cassette sub-family A member 2 isoform X1 [KO:K05642]
101801019  LGMN; legumain [KO:K01369] [EC:3.4.22.34]
101801092  GNS; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
101801719  ASAH1; acid ceramidase [KO:K12348] [EC:3.5.1.23]
101801736  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
101801880  CTSA; lysosomal protective protein [KO:K13289] [EC:3.4.16.5]
101802036  [KO:K01052] [EC:3.1.1.13]
101802167  ATP6V0D2; V-type proton ATPase subunit d 2 [KO:K02146]
101802475  CD164; sialomucin core protein 24 [KO:K06546]
101802501  WDR7; LOW QUALITY PROTEIN: WD repeat-containing protein 7 [KO:K24738]
101802752  [KO:K01319] [EC:3.4.21.20]
101802978  ARSB; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
101803026  NPC1; NPC intracellular cholesterol transporter 1 [KO:K12385]
101803168  CTSL; procathepsin L isoform X1 [KO:K01365] [EC:3.4.22.15]
101803900  MANBA; beta-mannosidase [KO:K01192] [EC:3.2.1.25]
101804055  AP3B1; AP-3 complex subunit beta-1 isoform X1 [KO:K12397]
101804172  MEAK7; MTOR-associated protein MEAK7 [KO:K27947]
101804173  [KO:K01382] [EC:3.4.23.34]
101804246  CTSZ; cathepsin Z [KO:K08568] [EC:3.4.18.1]
101804606  NCOA7; nuclear receptor coactivator 7 isoform X4 [KO:K25442]
101804681  GM2A; ganglioside GM2 activator [KO:K12383]
101804912  CTSH; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
101804994  AP3M1; AP-3 complex subunit mu-1 [KO:K12398]
101805028  ATP6V0D1; V-type proton ATPase subunit d 1 [KO:K02146]
101805141  CTSC; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
101805176  ATP6V0A1; V-type proton ATPase 116 kDa subunit a1 isoform X1 [KO:K02154]
101805206  IDS; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
106014259  [KO:K01197] [EC:3.2.1.35]
106020238  [KO:K12382]
110354702  SMPD1; LOW QUALITY PROTEIN: sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
113839605  [KO:K01365] [EC:3.4.22.15]
113839618  CLTB; LOW QUALITY PROTEIN: clathrin light chain B [KO:K04645]
113839970  NAGLU; LOW QUALITY PROTEIN: alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
113845291  [KO:K12316] [EC:3.2.1.20]
119712991  [KO:K13444] [EC:1.8.3.7]
119713205  GAA; LOW QUALITY PROTEIN: lysosomal alpha-glucosidase [KO:K12316] [EC:3.2.1.20]
119713207  SGSH; LOW QUALITY PROTEIN: N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
119713522  ENTPD4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
119713617  FUCA1; LOW QUALITY PROTEIN: tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
119713628  PPT1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
119713756  [KO:K01201] [EC:3.2.1.45]
119713757  [KO:K01201] [EC:3.2.1.45]
119713767  [KO:K01201] [EC:3.2.1.45]
119714087  [KO:K01205] [EC:3.2.1.50]
119714243  [KO:K04992]
119714244  [KO:K04992]
119714699  CD63; LOW QUALITY PROTEIN: CD63 antigen [KO:K06497]
119715046  AP1M2; AP-1 complex subunit mu-2 isoform X1 [KO:K12393]
119717653  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
119718238  [KO:K01197] [EC:3.2.1.35]
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
apla00511  Other glycan degradation
apla00531  Glycosaminoglycan degradation
apla04130  SNARE interactions in vesicular transport
apla04140  Autophagy - animal
apla04144  Endocytosis
KO pathway
ko04142   

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