KEGG   PATHWAY: nni04142
Entry
nni04142                    Pathway                                
Name
Lysosome - Nipponia nippon (crested ibis)
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
nni04142  Lysosome
nni04142

Other DBs
GO: 0005764
Organism
Nipponia nippon (crested ibis) [GN:nni]
Gene
104008686  HYAL3; hyaluronidase-3 [KO:K01197] [EC:3.2.1.35]
104008712  HYAL1; hyaluronidase-1 [KO:K01197] [EC:3.2.1.35]
104008746  HYAL2; hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
104008800  FUCA2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
104008852  NCOA7; nuclear receptor coactivator 7 isoform X1 [KO:K25442]
104009033  [KO:K02154]
104009598  CTSZ; cathepsin Z [KO:K08568] [EC:3.4.18.1]
104009633  ARSA; LOW QUALITY PROTEIN: arylsulfatase A [KO:K01134] [EC:3.1.6.8]
104009645  AP3D1; AP-3 complex subunit delta-1 [KO:K12396]
104009709  MAN2B1; lysosomal alpha-mannosidase [KO:K12311] [EC:3.2.1.24]
104009715  CLTCL1; clathrin heavy chain 2 isoform X1 [KO:K04646]
104009877  ATP6V0A1; V-type proton ATPase 116 kDa subunit a isoform 1 [KO:K02154]
104009928  NAGLU; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
104010107  SLC11A1; natural resistance-associated macrophage protein 1 [KO:K12347]
104010327  AP4B1; LOW QUALITY PROTEIN: AP-4 complex subunit beta-1 [KO:K12401]
104010349  CTSD; cathepsin D [KO:K01379] [EC:3.4.23.5]
104010556  AP1B1; AP-1 complex subunit beta-1 [KO:K12392]
104010833  WDR7; WD repeat-containing protein 7 isoform X1 [KO:K24738]
104010999  [KO:K01382] [EC:3.4.23.34]
104011053  GNS; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
104011152  CD164; sialomucin core protein 24 [KO:K06546]
104011181  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
104011755  CTSL; cathepsin L1 [KO:K01365] [EC:3.4.22.15]
104011790  AP4S1; AP-4 complex subunit sigma-1 [KO:K12403]
104011818  SPAM1; hyaluronidase PH-20 [KO:K01197] [EC:3.2.1.35]
104011823  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
104011835  [KO:K01197] [EC:3.2.1.35]
104011900  LAPTM4A; lysosomal-associated transmembrane protein 4A [KO:K12387]
104012153  GLB1; beta-galactosidase [KO:K12309] [EC:3.2.1.23]
104012179  CTNS; cystinosin isoform X1 [KO:K12386]
104012376  ATP6V0A4; V-type proton ATPase 116 kDa subunit a isoform 4 [KO:K02154]
104012550  ACP5; tartrate-resistant acid phosphatase type 5 [KO:K14379] [EC:3.1.3.2]
104013000  AP1S3; AP-1 complex subunit sigma-3 [KO:K12395]
104013157  [KO:K01052] [EC:3.1.1.13]
104013197  CTSE; cathepsin E [KO:K01382] [EC:3.4.23.34]
104013363  GNPTAB; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
104013387  HEXB; LOW QUALITY PROTEIN: beta-hexosaminidase subunit beta [KO:K12373] [EC:3.2.1.52]
104013546  PSAP; prosaposin [KO:K12382]
104013547  [KO:K12382]
104013573  [KO:K01052] [EC:3.1.1.13]
104013809  IGF2R; LOW QUALITY PROTEIN: cation-independent mannose-6-phosphate receptor [KO:K06564]
104013967  LIPA; lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
104013989  [KO:K01052] [EC:3.1.1.13]
104014065  CLTA; clathrin light chain A [KO:K04644]
104014253  GM2A; LOW QUALITY PROTEIN: ganglioside GM2 activator [KO:K12383]
104014292  ARSG; arylsulfatase G [KO:K12381] [EC:3.1.6.-]
104014328  GAA; lysosomal alpha-glucosidase [KO:K12316] [EC:3.2.1.20]
104014329  SGSH; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
104014432  CTSK; cathepsin K [KO:K01371] [EC:3.4.22.38]
104014433  [KO:K01368] [EC:3.4.22.27]
104014434  [KO:K01368] [EC:3.4.22.27]
104014568  DMXL1; LOW QUALITY PROTEIN: dmX-like protein 1 [KO:K24155]
104014579  M6PR; cation-dependent mannose-6-phosphate receptor [KO:K10089]
104014687  CTSB; cathepsin B [KO:K01363] [EC:3.4.22.1]
104014881  TPP1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
104014973  MCOLN1; mucolipin-1 [KO:K04992]
104015284  GGA2; ADP-ribosylation factor-binding protein GGA2 [KO:K12404]
104015291  GNPTG; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
104015353  GLA; alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
104015429  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
104015463  DNASE2B; deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
104015710  LAPTM5; lysosomal-associated transmembrane protein 5 [KO:K12387]
104015973  MFSD8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
104016078  AP3M2; AP-3 complex subunit mu-2 [KO:K12398]
104016092  GUSB; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
104016273  [KO:K01319] [EC:3.4.21.20]
104016464  PLA2G15; group XV phospholipase A2 [KO:K06129] [EC:3.1.1.5]
104016511  LAPTM4B; lysosomal-associated transmembrane protein 4B [KO:K12387]
104016578  CLTC; clathrin heavy chain 1 isoform X1 [KO:K04646]
104016697  AP3B2; AP-3 complex subunit beta-2 [KO:K12397]
104016788  HEXA; beta-hexosaminidase subunit alpha [KO:K12373] [EC:3.2.1.52]
104017009  SUMF1; sulfatase-modifying factor 1 [KO:K13444] [EC:1.8.3.7]
104017139  DMXL2; dmX-like protein 2 isoform X1 [KO:K24155]
104017143  AP4E1; AP-4 complex subunit epsilon-1 [KO:K12400]
104017184  AP3S2; AP-3 complex subunit sigma-2 [KO:K12399]
104017190  CTSH; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
104017387  CTSC; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
104017441  ATP6V0D1; V-type proton ATPase subunit d 1 [KO:K02146]
104017538  SORT1; sortilin [KO:K12388]
104017564  IDUA; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
104017575  AP3B1; LOW QUALITY PROTEIN: AP-3 complex subunit beta-1 [KO:K12397]
104017612  ARSB; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
104017858  FUCA1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
104017862  PPT1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
104018153  NPC1; Niemann-Pick C1 protein [KO:K12385]
104018334  CTSA; lysosomal protective protein [KO:K13289] [EC:3.4.16.5]
104018386  ABCA2; ATP-binding cassette sub-family A member 2 [KO:K05642]
104018468  [KO:K01319] [EC:3.4.21.20]
104018729  AP1M1; LOW QUALITY PROTEIN: AP-1 complex subunit mu-1 [KO:K12393]
104018797  [KO:K01365] [EC:3.4.22.15]
104018832  CLN5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
104018985  CLTB; LOW QUALITY PROTEIN: clathrin light chain B [KO:K04645]
104019072  IDS; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
104019091  LAMP2; lysosome-associated membrane glycoprotein 2 [KO:K06528]
104019186  SLC11A2; natural resistance-associated macrophage protein 2 [KO:K21398]
104019415  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
104019528  ENTPD4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
104019582  LAMP3; lysosome-associated membrane glycoprotein 3 [KO:K06562]
104019603  ABCB9; ATP-binding cassette sub-family B member 9 [KO:K05656]
104019709  ATP6V0A2; V-type proton ATPase 116 kDa subunit a isoform 2 isoform X1 [KO:K02154]
104019760  ATP6V1H; V-type proton ATPase subunit H isoform X1 [KO:K02144]
104019893  AP3S1; AP-3 complex subunit sigma-1 [KO:K12399]
104020027  AP3M1; AP-3 complex subunit mu-1 [KO:K12398]
104020466  ACP2; lysosomal acid phosphatase [KO:K14410] [EC:3.1.3.2]
104020491  [KO:K01201] [EC:3.2.1.45]
104020502  [KO:K01201] [EC:3.2.1.45]
104020625  AP4M1; AP-4 complex subunit mu-1 [KO:K12402]
104020668  GGA3; ADP-ribosylation factor-binding protein GGA3 [KO:K12404]
104020838  ASAH1; acid ceramidase [KO:K12348] [EC:3.5.1.23]
104021027  NPC2; epididymal secretory protein E1 [KO:K13443]
104021183  MANBA; beta-mannosidase [KO:K01192] [EC:3.2.1.25]
104021308  HGSNAT; heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
104021356  CTSO; cathepsin O [KO:K01374] [EC:3.4.22.42]
104021377  AGA; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
104021596  GGA1; ADP-ribosylation factor-binding protein GGA1 isoform X1 [KO:K12404]
104021651  NAGA; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
104021983  SLC17A5; sialin [KO:K12301]
104022210  LGMN; legumain [KO:K01369] [EC:3.4.22.34]
104022246  GALC; galactocerebrosidase [KO:K01202] [EC:3.2.1.46]
104022529  AP1S2; AP-1 complex subunit sigma-2 isoform X1 [KO:K12394]
104022785  ATP6V0D2; V-type proton ATPase subunit d 2 [KO:K02146]
104022815  [KO:K12399]
104023374  SCARB2; lysosome membrane protein 2 [KO:K12384]
104023450  LITAF; lipopolysaccharide-induced tumor necrosis factor-alpha factor [KO:K19363]
104023534  NAGPA; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
104023551  AP1G1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
104023569  GALNS; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
104023593  TLDC1; TLD domain-containing protein 1 [KO:K27947]
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
nni00511  Other glycan degradation
nni00531  Glycosaminoglycan degradation
nni04130  SNARE interactions in vesicular transport
nni04140  Autophagy - animal
nni04144  Endocytosis
KO pathway
ko04142   

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