KEGG   PATHWAY: mnb04142
Entry
mnb04142                    Pathway                                
Name
Lysosome - Merops nubicus (carmine bee-eater)
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
mnb04142  Lysosome
mnb04142

Other DBs
GO: 0005764
Organism
Merops nubicus (carmine bee-eater) [GN:mnb]
Gene
103774695  ATP6V0A2; V-type proton ATPase 116 kDa subunit a isoform 2 [KO:K02154]
103778210  ATP6V0A1; V-type proton ATPase 116 kDa subunit a isoform 1 [KO:K02154]
103778089  ATP6V0A4; V-type proton ATPase 116 kDa subunit a isoform 4 isoform X1 [KO:K02154]
103775851  V-type proton ATPase subunit d 2 [KO:K02146]
103776789  V-type proton ATPase subunit d 1 [KO:K02146]
103773090  ATP6V1H; V-type proton ATPase subunit H isoform X1 [KO:K02144]
103773462  V-type proton ATPase subunit S1-like [KO:K03662]
103770556  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
103781156  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
103780232  DMXL1; dmX-like protein 1 [KO:K24155]
103775396  DMXL2; dmX-like protein 2 isoform X1 [KO:K24155]
103779976  NCOA7; nuclear receptor coactivator 7 [KO:K25442]
103778150  CTSB; cathepsin B [KO:K01363] [EC:3.4.22.1]
103768367  CTSC; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
103769933  CTSD; cathepsin D [KO:K01379] [EC:3.4.23.5]
103775751  CTSE; cathepsin E [KO:K01382] [EC:3.4.23.34]
103777806  cathepsin E-A-like [KO:K01382] [EC:3.4.23.34]
103770335  mast cell protease 1A-like [KO:K01319] [EC:3.4.21.20]
103774156  CTSL; cathepsin L1 [KO:K01365] [EC:3.4.22.15]
103772292  CTSO; cathepsin O [KO:K01374] [EC:3.4.22.42]
103780570  CTSS; cathepsin S [KO:K01368] [EC:3.4.22.27]
103781972  CTSZ; cathepsin Z [KO:K08568] [EC:3.4.18.1]
103772654  LGMN; legumain [KO:K01369] [EC:3.4.22.34]
103772866  TPP1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
103770858  GLA; alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
103768731  GLB1; beta-galactosidase [KO:K12309] [EC:3.2.1.23]
103774119  LOW QUALITY PROTEIN: glucosylceramidase-like [KO:K01201] [EC:3.2.1.45]
103778672  glucosylceramidase-like [KO:K01201] [EC:3.2.1.45]
103770325  IDUA; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
103774977  NAGA; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
103775229  GALC; galactocerebrosidase [KO:K01202] [EC:3.2.1.46]
103780517  FUCA2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
103775762  FUCA1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
103768484  HEXB; beta-hexosaminidase subunit beta [KO:K12373] [EC:3.2.1.52]
103776427  HEXA; beta-hexosaminidase subunit alpha [KO:K12373] [EC:3.2.1.52]
103773519  MANBA; beta-mannosidase [KO:K01192] [EC:3.2.1.25]
103780262  HYAL2; LOW QUALITY PROTEIN: hyaluronidase-2 [KO:K01197] [EC:3.2.1.35]
103768343  SPAM1; LOW QUALITY PROTEIN: hyaluronidase PH-20 [KO:K01197] [EC:3.2.1.35]
103768822  HYAL1; hyaluronidase-1 [KO:K01197] [EC:3.2.1.35]
103778052  hyaluronidase-1-like [KO:K01197] [EC:3.2.1.35]
103776695  GALNS; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
103773982  GNS; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
103781129  IDS; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
103782374  putative lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
103777684  LOW QUALITY PROTEIN: lysosomal acid lipase/cholesteryl ester hydrolase-like [KO:K01052] [EC:3.1.1.13]
103769137  PLA2G15; group XV phospholipase A2 [KO:K06129] [EC:3.1.1.5]
103768847  DNASE2B; deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
103773492  ACP2; lysosomal acid phosphatase [KO:K14410] [EC:3.1.3.2]
103773396  ASAH1; acid ceramidase [KO:K12348] [EC:3.5.1.23]
103769260  AGA; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
103782207  PSAP; prosaposin [KO:K12382]
103782208  LOW QUALITY PROTEIN: proactivator polypeptide-like [KO:K12382]
103779851  GM2A; ganglioside GM2 activator [KO:K12383]
103773962  PPT1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
103781099  LAMP2; lysosome-associated membrane glycoprotein 2 [KO:K06528]
103777534  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
103776496  LAMP3; lysosome-associated membrane glycoprotein 3 [KO:K06562]
103773251  SCARB2; lysosome membrane protein 2 [KO:K12384]
103780047  NPC1; Niemann-Pick C1 protein [KO:K12385]
103771624  NPC2; epididymal secretory protein E1 [KO:K13443]
103768139  CTNS; cystinosin isoform X1 [KO:K12386]
103771015  SLC17A5; sialin [KO:K12301]
103781519  SLC11A1; natural resistance-associated macrophage protein 1 [KO:K12347]
103774933  SLC11A2; natural resistance-associated macrophage protein 2 [KO:K21398]
103782540  LAPTM4A; lysosomal-associated transmembrane protein 4A [KO:K12387]
103778702  LAPTM5; lysosomal-associated transmembrane protein 5 isoform X1 [KO:K12387]
103778533  ABCB9; ATP-binding cassette sub-family B member 9 [KO:K05656]
103778502  sialomucin core protein 24-like [KO:K06546]
103770318  ENTPD4; ectonucleoside triphosphate diphosphohydrolase 4 [KO:K12305] [EC:3.6.1.6]
103768347  CLN5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
103770019  MFSD8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
103778195  HGSNAT; LOW QUALITY PROTEIN: heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
103774366  GNPTAB; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
103781015  NAGPA; LOW QUALITY PROTEIN: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
103769305  IGF2R; cation-independent mannose-6-phosphate receptor [KO:K06564]
103774589  M6PR; cation-dependent mannose-6-phosphate receptor [KO:K10089]
103771014  CLTA; clathrin light chain A [KO:K04644]
103776550  CLTB; clathrin light chain B [KO:K04645]
103768546  clathrin heavy chain 1-like isoform X1 [KO:K04646]
103775521  CLTC; clathrin heavy chain 1 isoform X1 [KO:K04646]
103775837  AP1G1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
103767932  AP-1 complex subunit beta-1 [KO:K12392]
103769590  AP1M1; AP-1 complex subunit mu-1 [KO:K12393]
103770862  AP1S2; AP-1 complex subunit sigma-2 isoform X1 [KO:K12394]
103770114  AP-1 complex subunit sigma-3-like [KO:K12395]
103777925  AP3D1; LOW QUALITY PROTEIN: AP-3 complex subunit delta-1 [KO:K12396]
103775212  AP-3 complex subunit beta-1-like [KO:K12397]
103782369  AP3B2; AP-3 complex subunit beta-2 [KO:K12397]
103773704  AP3M2; AP-3 complex subunit mu-2 [KO:K12398]
103781240  AP-3 complex subunit mu-1-like [KO:K12398]
103770240  AP4E1; LOW QUALITY PROTEIN: AP-4 complex subunit epsilon-1 [KO:K12400]
103778995  AP4B1; AP-4 complex subunit beta-1 [KO:K12401]
103769212  AP4S1; AP-4 complex subunit sigma-1 [KO:K12403]
103774394  GGA3; LOW QUALITY PROTEIN: ADP-ribosylation factor-binding protein GGA3 [KO:K12404]
103771591  GGA2; ADP-ribosylation factor-binding protein GGA2 [KO:K12404]
103771677  GGA1; ADP-ribosylation factor-binding protein GGA1 isoform X1 [KO:K12404]
103772311  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
mnb00511  Other glycan degradation
mnb00531  Glycosaminoglycan degradation
mnb04130  SNARE interactions in vesicular transport
mnb04140  Autophagy - animal
mnb04144  Endocytosis
KO pathway
ko04142   
LinkDB

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