KEGG   PATHWAY: amj04142
Entry
amj04142                    Pathway                                
Name
Lysosome - Alligator mississippiensis (American alligator)
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
amj04142  Lysosome
amj04142

Other DBs
GO: 0005764
Organism
Alligator mississippiensis (American alligator) [GN:amj]
Gene
102572518  ATP6V0A1; ATPase H+ transporting V0 subunit a1 [KO:K02154]
106736679  ATP6V0A4; ATPase H+ transporting V0 subunit a4 [KO:K02154]
102569694  ATP6V0A2; ATPase H+ transporting V0 subunit a2 [KO:K02154]
102559672  TCIRG1; T-cell immune regulator 1, ATPase H+ transporting V0 subunit a3 [KO:K02154]
102566859  ATP6V0D2; ATPase H+ transporting V0 subunit d2 [KO:K02146]
106736986  ATP6V0D1; ATPase H+ transporting V0 subunit d1 [KO:K02146]
102570066  ATP6V1H; ATPase H+ transporting V1 subunit H [KO:K02144]
102572825  V-type proton ATPase subunit S1 [KO:K03662]
102570085  ATP6AP1; ATPase H+ transporting accessory protein 1 [KO:K03662]
102573788  ATP6V0C; ATPase H+ transporting V0 subunit c [KO:K02155]
102557934  ATP6V0B; ATPase H+ transporting V0 subunit b [KO:K03661]
102566897  DMXL1; Dmx like 1 [KO:K24155]
106736646  DMXL2; Dmx like 2 [KO:K24155]
102570892  WDR7; WD repeat domain 7 [KO:K24738]
102559172  NCOA7; nuclear receptor coactivator 7 [KO:K25442]
102564952  CTSA; cathepsin A [KO:K13289] [EC:3.4.16.5]
102572879  lysosomal protective protein [KO:K13289] [EC:3.4.16.5]
102573171  CTSB; cathepsin B [KO:K01363] [EC:3.4.22.1]
102576717  CTSC; cathepsin C [KO:K01275] [EC:3.4.14.1]
102558679  CTSD; cathepsin D [KO:K01379] [EC:3.4.23.5]
102576563  cathepsin D [KO:K01379] [EC:3.4.23.5]
102567770  CTSE; cathepsin E [KO:K01382] [EC:3.4.23.34]
102566566  NOTS; cathepsin E-A [KO:K01382] [EC:3.4.23.34]
102558774  CTSF; cathepsin F [KO:K01373] [EC:3.4.22.41]
102561787  chymase-like [KO:K01319] [EC:3.4.21.20]
102567538  GZMM; granzyme M [KO:K01319] [EC:3.4.21.20]
102570566  CTSG; mast cell protease 1A [KO:K01319] [EC:3.4.21.20]
109283684  cathepsin G-like [KO:K01319] [EC:3.4.21.20]
102562017  mast cell protease 3 [KO:K01319] [EC:3.4.21.20]
102564481  CTSH; cathepsin H [KO:K01366] [EC:3.4.22.16]
109281035  CTSK; cathepsin K [KO:K01371] [EC:3.4.22.38]
102572965  CTSL; cathepsin L [KO:K01365] [EC:3.4.22.15]
102560893  cathepsin L1 [KO:K01365] [EC:3.4.22.15]
102566412  CTSO; cathepsin O [KO:K01374] [EC:3.4.22.42]
109283982  cathepsin S-like [KO:K01368] [EC:3.4.22.27]
102562033  CTSS; cathepsin S [KO:K01368] [EC:3.4.22.27]
106738633  CTSW; cathepsin W [KO:K08569] [EC:3.4.22.-]
102561646  CTSZ; cathepsin Z [KO:K08568] [EC:3.4.18.1]
102570177  LGMN; legumain [KO:K01369] [EC:3.4.22.34]
102560569  TPP1; tripeptidyl peptidase 1 [KO:K01279] [EC:3.4.14.9]
102565208  GLA; galactosidase alpha [KO:K01189] [EC:3.2.1.22]
102567630  GLB1; galactosidase beta 1 [KO:K12309] [EC:3.2.1.23]
102577078  GAA; glucosidase alpha, acid [KO:K12316] [EC:3.2.1.20]
102572123  lysosomal alpha-glucosidase-like [KO:K12316] [EC:3.2.1.20]
102572708  glucosylceramidase [KO:K01201] [EC:3.2.1.45]
102565590  GBA; glucosylceramidase [KO:K01201] [EC:3.2.1.45]
106739741  glucosylceramidase-like [KO:K01201] [EC:3.2.1.45]
102565029  IDUA; iduronidase, alpha-L- [KO:K01217] [EC:3.2.1.76]
102561061  NAGA; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
102568142  NAGLU; N-acetyl-alpha-glucosaminidase [KO:K01205] [EC:3.2.1.50]
102575324  GALC; galactosylceramidase [KO:K01202] [EC:3.2.1.46]
102576515  GUSB; glucuronidase beta [KO:K01195] [EC:3.2.1.31]
102575452  FUCA2; fucosidase, alpha-L- 2, plasma [KO:K01206] [EC:3.2.1.51]
102572793  FUCA1; fucosidase, alpha-L- 1, tissue [KO:K01206] [EC:3.2.1.51]
106737106  HEXB; hexosaminidase subunit beta [KO:K12373] [EC:3.2.1.52]
102577099  HEXA; hexosaminidase subunit alpha [KO:K12373] [EC:3.2.1.52]
102564843  MANBA; mannosidase beta [KO:K01192] [EC:3.2.1.25]
102562074  MAN2B1; mannosidase alpha class 2B member 1 [KO:K12311] [EC:3.2.1.24]
102572868  NEU1; neuraminidase 1 [KO:K01186] [EC:3.2.1.18]
109284220  SPAM1; sperm adhesion molecule 1 [KO:K01197] [EC:3.2.1.35]
102574839  HYAL4; hyaluronidase-4 [KO:K01197] [EC:3.2.1.35]
102574610  hyaluronidase-1-like [KO:K01197] [EC:3.2.1.35]
102557643  HYAL3; hyaluronoglucosaminidase 3 [KO:K01197] [EC:3.2.1.35]
102575064  HYAL2; hyaluronoglucosaminidase 2 [KO:K01197] [EC:3.2.1.35]
102574830  HYAL1; hyaluronoglucosaminidase 1 [KO:K01197] [EC:3.2.1.35]
106739791  ARSA; arylsulfatase A [KO:K01134] [EC:3.1.6.8]
106737251  ARSB; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
102567869  ARSG; arylsulfatase G [KO:K12381] [EC:3.1.6.-]
102560299  GALNS; galactosamine (N-acetyl)-6-sulfatase [KO:K01132] [EC:3.1.6.4]
102561583  GNS; glucosamine (N-acetyl)-6-sulfatase [KO:K01137] [EC:3.1.6.14]
102571433  IDS; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
102576386  SGSH; N-sulfoglucosamine sulfohydrolase [KO:K01565] [EC:3.10.1.1]
102576768  lysosomal acid lipase/cholesteryl ester hydrolase-like [KO:K01052] [EC:3.1.1.13]
102576001  lysosomal acid lipase/cholesteryl ester hydrolase-like [KO:K01052] [EC:3.1.1.13]
102565327  lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
102560328  lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
102565563  lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
102560092  lysosomal acid lipase/cholesteryl ester hydrolase [KO:K01052] [EC:3.1.1.13]
102562113  LIPA; lipase A, lysosomal acid type [KO:K01052] [EC:3.1.1.13]
102559717  PLA2G15; phospholipase A2 group XV [KO:K06129] [EC:3.1.1.5]
102571694  DNASE2B; deoxyribonuclease 2 beta [KO:K01158] [EC:3.1.22.1]
102569684  DNASE2; deoxyribonuclease 2, lysosomal [KO:K01158] [EC:3.1.22.1]
102571780  ACP2; acid phosphatase 2, lysosomal [KO:K14410] [EC:3.1.3.2]
102573168  ACP5; acid phosphatase 5, tartrate resistant [KO:K14379] [EC:3.1.3.2]
106740329  SMPD1; sphingomyelin phosphodiesterase 1 [KO:K12350] [EC:3.1.4.12]
102566045  ASAH1; N-acylsphingosine amidohydrolase 1 [KO:K12348] [EC:3.5.1.23]
102565336  AGA; aspartylglucosaminidase [KO:K01444] [EC:3.5.1.26]
102575296  N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
102570959  prosaposin [KO:K12382]
102571192  PSAP; prosaposin [KO:K12382]
102568452  GM2A; GM2 ganglioside activator [KO:K12383]
102570797  PPT2; palmitoyl-protein thioesterase 2 [KO:K01074] [EC:3.1.2.22]
102566224  PPT1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
102558578  LAMP1; lysosomal associated membrane protein 1 [KO:K06528]
102568123  LAMP2; lysosomal associated membrane protein 2 [KO:K06528]
102565192  LAMP3; lysosomal associated membrane protein 3 [KO:K06562]
102565776  CD68; CD68 molecule [KO:K06501]
102558948  CD63; CD63 molecule [KO:K06497]
102560984  tetraspanin-7 [KO:K06497]
102570343  SCARB2; scavenger receptor class B member 2 [KO:K12384]
102570133  NPC1; NPC intracellular cholesterol transporter 1 [KO:K12385]
102559560  NPC2; NPC intracellular cholesterol transporter 2 [KO:K13443]
102562512  CTNS; cystinosin, lysosomal cystine transporter [KO:K12386]
102566858  SLC17A5; solute carrier family 17 member 5 [KO:K12301]
106736950  SLC11A1; solute carrier family 11 member 1 [KO:K12347]
102575517  SLC11A2; solute carrier family 11 member 2 [KO:K21398]
102565855  LAPTM4A; lysosomal protein transmembrane 4 alpha [KO:K12387]
102570730  LAPTM5; lysosomal protein transmembrane 5 [KO:K12387]
102570118  LAPTM4B; lysosomal protein transmembrane 4 beta [KO:K12387]
102569550  ABCA2; ATP binding cassette subfamily A member 2 [KO:K05642]
102570238  ABCB9; ATP binding cassette subfamily B member 9 [KO:K05656]
106737406  CD164; CD164 molecule [KO:K06546]
102558389  ENTPD4; ectonucleoside triphosphate diphosphohydrolase 4 [KO:K12305] [EC:3.6.1.6]
102560367  SORT1; sortilin 1 [KO:K12388]
102567588  CLN3; CLN3, battenin [KO:K12389]
102567515  CLN5; ceroid-lipofuscinosis, neuronal 5 [KO:K12390]
102561037  MFSD8; major facilitator superfamily domain containing 8 [KO:K12307]
102558466  major facilitator superfamily domain-containing protein 8 [KO:K12307]
102558169  BMS1; heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
102567230  HGSNAT; heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
102562381  SUMF1; sulfatase modifying factor 1 [KO:K13444] [EC:1.8.3.7]
102569913  GNPTAB; N-acetylglucosamine-1-phosphate transferase alpha and beta subunits [KO:K08239] [EC:2.7.8.17]
102576470  GNPTG; N-acetylglucosamine-1-phosphate transferase gamma subunit [KO:K10087]
102559983  NAGPA; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
102561234  IGF2R; insulin like growth factor 2 receptor [KO:K06564]
102576143  M6PR; mannose-6-phosphate receptor, cation dependent [KO:K10089]
102563361  CLTA; clathrin light chain A [KO:K04644]
102563380  CLTB; clathrin light chain B [KO:K04645]
102570092  CLTC; clathrin heavy chain [KO:K04646]
102573001  CLTCL1; clathrin heavy chain like 1 [KO:K04646]
102561371  AP1G1; adaptor related protein complex 1 gamma 1 subunit [KO:K12391]
102558940  AP1B1; adaptor related protein complex 1 beta 1 subunit [KO:K12392]
102561685  AP1M2; adaptor related protein complex 1 mu 2 subunit [KO:K12393]
106736695  AP1M1; adaptor related protein complex 1 mu 1 subunit [KO:K12393]
102560773  AP1S1; AP-1 complex subunit sigma-1A [KO:K12394]
102567825  AP1S2; adaptor related protein complex 1 sigma 2 subunit [KO:K12394]
102566806  AP1S3; adaptor related protein complex 1 sigma 3 subunit [KO:K12395]
102569911  AP3D1; adaptor related protein complex 3 delta 1 subunit [KO:K12396]
102570932  AP3B1; adaptor related protein complex 3 beta 1 subunit [KO:K12397]
102563947  AP3B2; adaptor related protein complex 3 beta 2 subunit [KO:K12397]
102560718  AP3M2; adaptor related protein complex 3 mu 2 subunit [KO:K12398]
102569260  AP3M1; adaptor related protein complex 3 mu 1 subunit [KO:K12398]
102562306  AP3S1; adaptor related protein complex 3 sigma 1 subunit [KO:K12399]
109284860  AP-3 complex subunit sigma-2-like [KO:K12399]
109280736  AP-3 complex subunit sigma-2-like [KO:K12399]
102565805  AP4E1; adaptor related protein complex 4 epsilon 1 subunit [KO:K12400]
102574254  AP4B1; adaptor related protein complex 4 beta 1 subunit [KO:K12401]
102559325  AP-4 complex subunit mu-1 [KO:K12402]
102566046  AP4S1; adaptor related protein complex 4 sigma 1 subunit [KO:K12403]
102562572  GGA2; golgi associated, gamma adaptin ear containing, ARF binding protein 2 [KO:K12404]
102566552  GGA1; golgi associated, gamma adaptin ear containing, ARF binding protein 1 [KO:K12404]
102571655  GGA3; golgi associated, gamma adaptin ear containing, ARF binding protein 3 [KO:K12404]
102577120  MCOLN1; mucolipin 1 [KO:K04992]
102570574  LITAF; lipopolysaccharide induced TNF 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
amj00511  Other glycan degradation
amj00531  Glycosaminoglycan degradation
amj04130  SNARE interactions in vesicular transport
amj04140  Autophagy - animal
amj04144  Endocytosis
KO pathway
ko04142   
LinkDB

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