KEGG   PATHWAY: leri04142
Entry
leri04142                   Pathway                                
Name
Lysosome - Leucoraja erinacea (little skate)
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
leri04142  Lysosome
leri04142

Other DBs
GO: 0005764
Organism
Leucoraja erinacea (little skate) [GN:leri]
Gene
129709237  atp6v0a2b; V-type proton ATPase 116 kDa subunit a [KO:K02154]
129710264  V-type proton ATPase 116 kDa subunit a 1 isoform X1 [KO:K02154]
129706233  V-type proton ATPase 116 kDa subunit a 4-like [KO:K02154]
129705100  V-type proton ATPase subunit d 1 [KO:K02146]
129709797  LOW QUALITY PROTEIN: V-type proton ATPase subunit d 1-like [KO:K02146]
129696295  atp6v1h; V-type proton ATPase subunit H [KO:K02144]
129706183  V-type proton ATPase subunit S1-like [KO:K03662]
129715244  V-type proton ATPase subunit S1-like [KO:K03662]
129706897  atp6v0cb; ATPase H+ transporting V0 subunit cb [KO:K02155]
129700869  atp6v0b; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
129694298  dmX-like protein 1 [KO:K24155]
129712589  dmxl2; dmX-like protein 2 isoform X1 [KO:K24155]
129714210  WD repeat-containing protein 7 isoform X1 [KO:K24738]
129697281  nuclear receptor coactivator 7-like isoform X1 [KO:K25442]
129705241  lysosomal protective protein-like [KO:K13289] [EC:3.4.16.5]
129705242  lysosomal protective protein-like [KO:K13289] [EC:3.4.16.5]
129707211  ctsa; lysosomal protective protein isoform X1 [KO:K13289] [EC:3.4.16.5]
129699887  LOW QUALITY PROTEIN: cathepsin B-like [KO:K01363] [EC:3.4.22.1]
129698245  ctsc; dipeptidyl peptidase 1 isoform X1 [KO:K01275] [EC:3.4.14.1]
129705743  ctsd; cathepsin D [KO:K01379] [EC:3.4.23.5]
129713901  cathepsin D-like [KO:K01379] [EC:3.4.23.5]
129708909  cathepsin E-like [KO:K01382] [EC:3.4.23.34]
129706423  cathepsin E-B-like [KO:K01382] [EC:3.4.23.34]
129712712  ctsh; pro-cathepsin H [KO:K01366] [EC:3.4.22.16]
129711259  procathepsin L-like [KO:K01371] [EC:3.4.22.38]
129695723  ctsla; cathepsin La [KO:K01365] [EC:3.4.22.15]
129709920  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
129711248  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
129711254  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
129711256  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
129711258  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
129711260  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
129711282  procathepsin L-like [KO:K01365] [EC:3.4.22.15]
129703329  cathepsin O-like [KO:K01374] [EC:3.4.22.42]
129711281  procathepsin L-like [KO:K01368] [EC:3.4.22.27]
129715877  cathepsin F-like [KO:K08569] [EC:3.4.22.-]
129707196  ctsz; cathepsin Z [KO:K08568] [EC:3.4.18.1]
129700579  legumain-like [KO:K01369] [EC:3.4.22.34]
129700145  tpp1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
129710798  beta-galactosidase-like [KO:K12309] [EC:3.2.1.23]
129706825  gaa2; lysosomal alpha-glucosidase [KO:K12316] [EC:3.2.1.20]
129708287  lysosomal alpha-glucosidase-like isoform X1 [KO:K12316] [EC:3.2.1.20]
129708288  lysosomal alpha-glucosidase-like isoform X1 [KO:K12316] [EC:3.2.1.20]
129716424  gba; lysosomal acid glucosylceramidase [KO:K01201] [EC:3.2.1.45]
129704107  idua; alpha-L-iduronidase isoform X1 [KO:K01217] [EC:3.2.1.76]
129713764  naga; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
129707010  alpha-N-acetylgalactosaminidase-like [KO:K01204] [EC:3.2.1.49]
129710049  naglu; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
129693404  galactocerebrosidase-like isoform X1 [KO:K01202] [EC:3.2.1.46]
129710804  gusb; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
129709699  tissue alpha-L-fucosidase-like [KO:K01206] [EC:3.2.1.51]
129699385  fuca2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
129695306  hexb; beta-hexosaminidase subunit beta isoform X1 [KO:K12373] [EC:3.2.1.52]
129696655  manba; LOW QUALITY PROTEIN: beta-mannosidase [KO:K01192] [EC:3.2.1.25]
129714513  man2b1; lysosomal alpha-mannosidase [KO:K12311] [EC:3.2.1.24]
129694595  neu1; sialidase-1 [KO:K01186] [EC:3.2.1.18]
129708906  hyaluronidase PH-20-like [KO:K01197] [EC:3.2.1.35]
129706190  hyal6; hyaluronoglucosaminidase 6 [KO:K01197] [EC:3.2.1.35]
129706191  hyaluronidase-5-like [KO:K01197] [EC:3.2.1.35]
129704631  hyaluronidase-like [KO:K01197] [EC:3.2.1.35]
129704633  hyaluronidase-4-like [KO:K01197] [EC:3.2.1.35]
129704639  hyaluronidase-2-like isoform X1 [KO:K01197] [EC:3.2.1.35]
129704758  hyaluronidase-1-like isoform X1 [KO:K01197] [EC:3.2.1.35]
129704759  hyaluronidase-1-like [KO:K01197] [EC:3.2.1.35]
129704917  hyaluronidase-like [KO:K01197] [EC:3.2.1.35]
129707864  arylsulfatase A-like [KO:K01134] [EC:3.1.6.8]
129708056  arylsulfatase A-like [KO:K01134] [EC:3.1.6.8]
129694849  arsb; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
129708279  arsg; arylsulfatase G isoform X1 [KO:K12381] [EC:3.1.6.-]
129715073  galns; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
129713195  gnsb; glucosamine (N-acetyl)-6-sulfatase (Sanfilippo disease IIID), b [KO:K01137] [EC:3.1.6.14]
129706463  gnsa; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
129702287  ids; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
129708196  sgsh; LOW QUALITY PROTEIN: N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
129704258  lipf; gastric triacylglycerol lipase [KO:K01052] [EC:3.1.1.13]
129705134  pla2g15; group XV phospholipase A2 [KO:K06129] [EC:3.1.1.5]
129700698  dnase2b; deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
129714346  deoxyribonuclease-2-alpha-like [KO:K01158] [EC:3.1.22.1]
129705910  prostatic acid phosphatase-like isoform X1 [KO:K14410] [EC:3.1.3.2]
129705913  lysosomal acid phosphatase-like [KO:K14410] [EC:3.1.3.2]
129700772  acp5b; tartrate-resistant acid phosphatase type 5b [KO:K14379] [EC:3.1.3.2]
129714390  acp5a; tartrate-resistant acid phosphatase type 5a isoform X1 [KO:K14379] [EC:3.1.3.2]
129698345  smpd1; LOW QUALITY PROTEIN: sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
129697062  asah1b; acid ceramidase [KO:K12348] [EC:3.5.1.23]
129716206  N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase- like isoform X1 [KO:K01444] [EC:3.5.1.26]
129716207  LOW QUALITY PROTEIN: N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase-like [KO:K01444] [EC:3.5.1.26]
129713073  psap; prosaposin [KO:K12382]
129713419  prosaposin-like [KO:K12382]
129701471  ganglioside GM2 activator-like [KO:K12383]
129701472  uncharacterized protein LOC129701472 [KO:K12383]
129712156  ganglioside GM2 activator-like [KO:K12383]
129712160  ganglioside GM2 activator-like [KO:K12383]
129709717  palmitoyl-protein thioesterase 1-like isoform X1 [KO:K01074] [EC:3.1.2.22]
129709719  palmitoyl-protein thioesterase 1-like [KO:K01074] [EC:3.1.2.22]
129715886  ppt2b; lysosomal thioesterase PPT2 [KO:K01074] [EC:3.1.2.22]
129702070  lamp2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
129702757  lamp1a; lysosome-associated membrane glycoprotein 1a [KO:K06528]
129703194  lamp3; lysosome-associated membrane glycoprotein 3 isoform X1 [KO:K06562]
129698789  CD63 antigen-like isoform X1 [KO:K06497]
129714752  cd63; CD63 antigen [KO:K06497]
129702781  lysosome membrane protein 2-like [KO:K12384]
129699746  lysosome membrane protein 2-like [KO:K12384]
129696395  npc1; NPC intracellular cholesterol transporter 1 [KO:K12385]
129700002  NPC intracellular cholesterol transporter 2-like [KO:K13443]
129700003  NPC intracellular cholesterol transporter 2-like [KO:K13443]
129710938  cystinosin-like [KO:K12386]
129711300  ctns; LOW QUALITY PROTEIN: cystinosin [KO:K12386]
129697018  slc17a5; sialin [KO:K12301]
129714625  natural resistance-associated macrophage protein 2-like isoform X1 [KO:K21398]
129714754  natural resistance-associated macrophage protein 2-like [KO:K21398]
129709879  lysosomal-associated transmembrane protein 4A-like isoform X1 [KO:K12387]
129696435  laptm4b; lysosomal-associated transmembrane protein 4B [KO:K12387]
129697146  laptm4a; lysosomal-associated transmembrane protein 4A [KO:K12387]
129712124  abca2; ATP-binding cassette sub-family A member 2 [KO:K05642]
129696884  cd164; sialomucin core protein 24 isoform X1 [KO:K06546]
129713221  entpd4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
129708949  sortilin-like [KO:K12388]
129706207  sortilin-like [KO:K12388]
129697969  cln5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
129703623  mfsd8l1; major facilitator superfamily domain-containing protein 8 isoform X1 [KO:K12307]
129704496  mfsd8; major facilitator superfamily domain-containing protein 8 isoform X1 [KO:K12307]
129701218  LOW QUALITY PROTEIN: heparan-alpha-glucosaminide N-acetyltransferase-like [KO:K10532] [EC:2.3.1.78]
129712936  si:dkey-192p21.6; heparan-alpha-glucosaminide N-acetyltransferase [KO:K10532] [EC:2.3.1.78]
129704554  sumf1; formylglycine-generating enzyme [KO:K13444] [EC:1.8.3.7]
129706317  gnptab; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
129706779  gnptg; N-acetylglucosamine-1-phosphotransferase subunit gamma isoform X1 [KO:K10087]
129696161  nagpa; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
129699544  igf2r; LOW QUALITY PROTEIN: cation-independent mannose-6-phosphate receptor [KO:K06564]
129702089  clathrin light chain A-like isoform X1 [KO:K04644]
129701697  clathrin light chain B-like [KO:K04645]
129709218  cltcl1; clathrin heavy chain 1 isoform X1 [KO:K04646]
129710450  clathrin heavy chain 1-like [KO:K04646]
129705476  ap1g1; AP-1 complex subunit gamma-1 [KO:K12391]
129707179  AP-1 complex subunit gamma-1-like [KO:K12391]
129709453  ap1b1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
129711235  AP-1 complex subunit mu-1 [KO:K12393]
129700797  AP-1 complex subunit mu-1-like [KO:K12393]
129700915  AP-1 complex subunit mu-1-like isoform X1 [KO:K12393]
129714394  AP-1 complex subunit mu-2 [KO:K12393]
129702783  AP-1 complex subunit sigma-2 isoform X1 [KO:K12394]
129715286  ap1s1; AP-1 complex subunit sigma-1A isoform X1 [KO:K12394]
129703715  ap1s3a; AP-1 complex subunit sigma-3a isoform X1 [KO:K12395]
129711132  ap3d1; LOW QUALITY PROTEIN: AP-3 complex subunit delta-1 [KO:K12396]
129694800  ap3b1a; AP-3 complex subunit beta-1 [KO:K12397]
129713537  AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
129713326  AP-3 complex subunit mu-2 [KO:K12398]
129712853  ap3m2; AP-3 complex subunit mu-2 isoform X1 [KO:K12398]
129695819  AP-3 complex subunit sigma-1 isoform X1 [KO:K12399]
129712692  AP-3 complex subunit sigma-2-like isoform X1 [KO:K12399]
129712586  ap4e1; LOW QUALITY PROTEIN: AP-4 complex subunit epsilon-1 [KO:K12400]
129708604  ap4b1; AP-4 complex subunit beta-1 [KO:K12401]
129694125  ap4m1; AP-4 complex subunit mu-1 [KO:K12402]
129700299  ap4s1; AP-4 complex subunit sigma-1 [KO:K12403]
129713952  gga1; ADP-ribosylation factor-binding protein GGA1 isoform X1 [KO:K12404]
129706798  ADP-ribosylation factor-binding protein GGA1-like isoform X1 [KO:K12404]
129708351  gga3b; ADP-ribosylation factor-binding protein GGA3 isoform X1 [KO:K12404]
129714402  mcoln1a; mucolipin-1a [KO:K04992]
129706734  LITAF domain-containing protein-like [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
leri00511  Other glycan degradation
leri00531  Glycosaminoglycan degradation
leri04130  SNARE interactions in vesicular transport
leri04140  Autophagy - animal
leri04144  Endocytosis
KO pathway
ko04142   
LinkDB

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