KEGG   PATHWAY: oda04142
Entry
oda04142                    Pathway                                
Name
Lysosome - Oryx dammah (scimitar-horned oryx)
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
oda04142  Lysosome
oda04142

Other DBs
GO: 0005764
Organism
Oryx dammah (scimitar-horned oryx) [GN:oda]
Gene
120877631  ATP6V0A4; V-type proton ATPase 116 kDa subunit a [KO:K02154]
120874794  TCIRG1; V-type proton ATPase 116 kDa subunit a3 isoform X1 [KO:K02154]
120871019  ATP6V0A2; V-type proton ATPase 116 kDa subunit a2 [KO:K02154]
120867069  ATP6V0A1; V-type proton ATPase 116 kDa subunit a1 isoform X1 [KO:K02154]
120878524  ATP6V0D2; V-type proton ATPase subunit d 2 [KO:K02146]
120872737  ATP6V0D1; V-type proton ATPase subunit d 1 [KO:K02146]
120878573  ATP6V1H; V-type proton ATPase subunit H isoform X1 [KO:K02144]
120881819  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
120873700  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
120856270  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
120852989  DMXL2; dmX-like protein 2 isoform X1 [KO:K24155]
120864669  DMXL1; dmX-like protein 1 isoform X1 [KO:K24155]
120880902  WDR7; WD repeat-containing protein 7 isoform X1 [KO:K24738]
120862855  NCOA7; nuclear receptor coactivator 7 isoform X1 [KO:K25442]
120869514  CTSA; lysosomal protective protein isoform X1 [KO:K13289] [EC:3.4.16.5]
120857022  CTSB; cathepsin B isoform X1 [KO:K01363] [EC:3.4.22.1]
120874825  CTSC; dipeptidyl peptidase 1 isoform X1 [KO:K01275] [EC:3.4.14.1]
120874183  CTSD; cathepsin D [KO:K01379] [EC:3.4.23.5]
120874747  CTSF; cathepsin F isoform X1 [KO:K01373] [EC:3.4.22.41]
120875430  cathepsin G-like [KO:K01319] [EC:3.4.21.20]
120875562  CTSH; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
120855928  CTSK; cathepsin K [KO:K01371] [EC:3.4.22.38]
120867201  procathepsin L [KO:K01365] [EC:3.4.22.15]
120866989  CTSL; procathepsin L [KO:K01365] [EC:3.4.22.15]
120871380  CTSO; cathepsin O [KO:K01374] [EC:3.4.22.42]
120855927  CTSS; cathepsin S [KO:K01368] [EC:3.4.22.27]
120874665  CTSW; cathepsin W isoform X1 [KO:K08569] [EC:3.4.22.-]
120869382  CTSZ; cathepsin Z [KO:K08568] [EC:3.4.18.1]
120872000  NAPSA; napsin-A [KO:K08565] [EC:3.4.23.-]
120874982  LGMN; legumain [KO:K01369] [EC:3.4.22.34]
120876542  TPP1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
120881310  GLA; alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
120867861  beta-galactosidase isoform X1 [KO:K12309] [EC:3.2.1.23]
120866837  GAA; lysosomal alpha-glucosidase [KO:K12316] [EC:3.2.1.20]
120855733  GBA; lysosomal acid glucosylceramidase [KO:K01201] [EC:3.2.1.45]
120861850  IDUA; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
120857579  NAGA; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
120867079  NAGLU; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
120853561  GALC; galactocerebrosidase isoform X1 [KO:K01202] [EC:3.2.1.46]
120882707  LOW QUALITY PROTEIN: beta-glucuronidase-like [KO:K01195] [EC:3.2.1.31]
120877954  GUSB; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
120862565  FUCA2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
120855051  FUCA1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
120879649  HEXB; beta-hexosaminidase subunit beta isoform X1 [KO:K12373] [EC:3.2.1.52]
120860852  beta-hexosaminidase subunit alpha isoform X1 [KO:K12373] [EC:3.2.1.52]
120853507  HEXA; beta-hexosaminidase subunit alpha [KO:K12373] [EC:3.2.1.52]
120861870  MANBA; beta-mannosidase [KO:K01192] [EC:3.2.1.25]
120864030  MAN2B1; lysosomal alpha-mannosidase [KO:K12311] [EC:3.2.1.24]
120870568  NEU1; sialidase-1 [KO:K01186] [EC:3.2.1.18]
120877304  hyaluronidase PH-20-like [KO:K01197] [EC:3.2.1.35]
120877537  HYAL4; hyaluronidase-4 [KO:K01197] [EC:3.2.1.35]
120877539  hyaluronidase PH-20-like [KO:K01197] [EC:3.2.1.35]
120868296  HYAL2; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
120868299  HYAL1; hyaluronidase-1 [KO:K01197] [EC:3.2.1.35]
120868300  HYAL3; hyaluronidase-3 isoform X1 [KO:K01197] [EC:3.2.1.35]
120857789  ARSA; arylsulfatase A [KO:K01134] [EC:3.1.6.8]
120852580  ARSB; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
120866599  ARSG; arylsulfatase G isoform X1 [KO:K12381] [EC:3.1.6.-]
120872955  GALNS; N-acetylgalactosamine-6-sulfatase isoform X1 [KO:K01132] [EC:3.1.6.4]
120857690  GNS; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
120881766  IDS; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
120866841  SGSH; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
120873786  LIPA; lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
120872733  PLA2G15; phospholipase A2 group XV [KO:K06129] [EC:3.1.1.5]
120864042  DNASE2; deoxyribonuclease-2-alpha [KO:K01158] [EC:3.1.22.1]
120856551  DNASE2B; deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
120876951  ACP2; lysosomal acid phosphatase isoform X1 [KO:K14410] [EC:3.1.3.2]
120863924  ACP5; tartrate-resistant acid phosphatase type 5 [KO:K14379] [EC:3.1.3.2]
120876551  SMPD1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
120865766  ASAH1; acid ceramidase [KO:K12348] [EC:3.5.1.23]
120860538  N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase- like [KO:K01444] [EC:3.5.1.26]
120865842  AGA; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
120861795  PSAPL1; proactivator polypeptide-like 1 [KO:K12382]
120865328  prosaposin isoform X1 [KO:K12382]
120863392  GM2A; ganglioside GM2 activator [KO:K12383]
120870590  PPT2; lysosomal thioesterase PPT2 isoform X1 [KO:K01074] [EC:3.1.2.22]
120856363  PPT1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
120883256  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
120881514  LAMP2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
120871746  LAMP3; lysosome-associated membrane glycoprotein 3 isoform X1 [KO:K06562]
120866043  CD68; macrosialin [KO:K06501]
120881705  CD63 antigen-like [KO:K06497]
120857408  CD63; CD63 antigen [KO:K06497]
120861464  SCARB2; lysosome membrane protein 2 [KO:K12384]
120880833  NPC intracellular cholesterol transporter 1 [KO:K12385]
120852723  NPC2; NPC intracellular cholesterol transporter 2 [KO:K13443]
120866175  CTNS; cystinosin [KO:K12386]
120860407  sialin isoform X1 [KO:K12301]
120862889  SLC17A5; sialin isoform X1 [KO:K12301]
120854379  SLC11A1; natural resistance-associated macrophage protein 1 isoform X1 [KO:K12347]
120858106  natural resistance-associated macrophage protein 2-like [KO:K21398]
120858108  natural resistance-associated macrophage protein 2-like [KO:K21398]
120858173  natural resistance-associated macrophage protein 2 isoform X1 [KO:K21398]
120878450  LAPTM4B; lysosomal-associated transmembrane protein 4B [KO:K12387]
120851910  LAPTM4A; lysosomal-associated transmembrane protein 4A [KO:K12387]
120854506  LAPTM5; lysosomal-associated transmembrane protein 5 [KO:K12387]
120863099  lysosomal-associated transmembrane protein 4B-like [KO:K12387]
120860785  ATP-binding cassette sub-family A member 2 isoform X1 [KO:K05642]
120860796  ATP-binding cassette sub-family A member 2 isoform X1 [KO:K05642]
120871034  ABCB9; ATP-binding cassette sub-family B member 9 [KO:K05656]
120862522  CD164; sialomucin core protein 24 isoform X1 [KO:K06546]
120865731  ENTPD4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
120856739  SORT1; sortilin isoform X1 [KO:K12388]
120876907  CLN3; battenin isoform X1 [KO:K12389]
120883025  CLN5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
120870950  MFSD8; major facilitator superfamily domain-containing protein 8 isoform X1 [KO:K12307]
120865863  HGSNAT; heparan-alpha-glucosaminide N-acetyltransferase isoform X1 [KO:K10532] [EC:2.3.1.78]
120867667  SUMF1; formylglycine-generating enzyme [KO:K13444] [EC:1.8.3.7]
120858668  GNPTAB; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
120872859  GNPTG; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
120874707  NAGPA; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
120862818  IGF2R; cation-independent mannose-6-phosphate receptor [KO:K06564]
120858794  M6PR; cation-dependent mannose-6-phosphate receptor isoform X1 [KO:K10089]
120882921  CLTA; clathrin light chain A isoform X1 [KO:K04644]
120863883  CLTB; clathrin light chain B isoform X1 [KO:K04645]
120866439  CLTC; clathrin heavy chain 1 isoform X1 [KO:K04646]
120853447  AP1G2; AP-1 complex subunit gamma-like 2 isoform X1 [KO:K12391]
120872660  AP1G1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
120871474  AP1B1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
120863968  AP1M2; AP-1 complex subunit mu-2 isoform X1 [KO:K12393]
120864191  AP1M1; AP-1 complex subunit mu-1 [KO:K12393]
120882553  AP1S2; AP-1 complex subunit sigma-2 isoform X1 [KO:K12394]
120878992  AP1S1; AP-1 complex subunit sigma-1A [KO:K12394]
120854462  AP1S3; AP-1 complex subunit sigma-3 [KO:K12395]
120864759  AP3D1; AP-3 complex subunit delta-1 [KO:K12396]
120852583  AP3B1; AP-3 complex subunit beta-1 [KO:K12397]
120875584  AP3B2; AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
120865294  AP3M1; AP-3 complex subunit mu-1 [KO:K12398]
120865685  AP3M2; AP-3 complex subunit mu-2 [KO:K12398]
120875626  AP-3 complex subunit sigma-2 [KO:K12399]
120852631  AP-3 complex subunit sigma-1 isoform X1 [KO:K12399]
120860981  AP-3 complex subunit sigma-1 isoform X1 [KO:K12399]
120865798  AP-3 complex subunit sigma-1-like [KO:K12399]
120852984  AP4E1; AP-4 complex subunit epsilon-1 [KO:K12400]
120856052  AP4B1; AP-4 complex subunit beta-1 [KO:K12401]
120879874  AP4M1; AP-4 complex subunit mu-1 [KO:K12402]
120875401  AP4S1; AP-4 complex subunit sigma-1 [KO:K12403]
120882572  GGA2; ADP-ribosylation factor-binding protein GGA2 [KO:K12404]
120858456  GGA1; ADP-ribosylation factor-binding protein GGA1 [KO:K12404]
120866733  GGA3; ADP-ribosylation factor-binding protein GGA3 isoform X1 [KO:K12404]
120863913  MCOLN1; mucolipin-1 isoform X1 [KO:K04992]
120855788  LITAF; lipopolysaccharide-induced tumor necrosis factor-alpha factor [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
oda00511  Other glycan degradation
oda00531  Glycosaminoglycan degradation
oda04130  SNARE interactions in vesicular transport
oda04140  Autophagy - animal
oda04144  Endocytosis
KO pathway
ko04142   
LinkDB

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