KEGG   PATHWAY: rtem04142
Entry
rtem04142                   Pathway                                
Name
Lysosome - Rana temporaria (common frog)
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
rtem04142  Lysosome
rtem04142

Other DBs
GO: 0005764
Organism
Rana temporaria (common frog) [GN:rtem]
Gene
120908951  [KO:K12382]
120908954  SLC29A3; equilibrative nucleoside transporter 3 [KO:K15014]
120909047  AP3M1; AP-3 complex subunit mu-1 [KO:K12398]
120909087  BORCS8; BLOC-1-related complex subunit 8 isoform X1 [KO:K20822]
120909175  [KO:K20456]
120909274  TCIRG1; V-type proton ATPase 116 kDa subunit a3 [KO:K02154]
120909938  [KO:K01319] [EC:3.4.21.20]
120910441  [KO:K10532] [EC:2.3.1.78]
120913078  GLA; alpha-galactosidase A [KO:K01189] [EC:3.2.1.22]
120913088  [KO:K16185]
120913127  KXD1; kxDL motif-containing protein 1 [KO:K20818]
120913182  [KO:K07897]
120913188  ATP6V1G1; V-type proton ATPase subunit G 1 [KO:K02152]
120913247  PPT2; lysosomal thioesterase PPT2 isoform X1 [KO:K01074] [EC:3.1.2.22]
120913259  ATP6V1G2; V-type proton ATPase subunit G 2 [KO:K02152]
120913260  NEU1; sialidase-1 [KO:K01186] [EC:3.2.1.18]
120913278  [KO:K12393]
120913407  AP3D1; AP-3 complex subunit delta-1 isoform X1 [KO:K12396]
120913567  BLOC1S3; biogenesis of lysosome-related organelles complex 1 subunit 3 [KO:K20186]
120913587  VAMP7; vesicle-associated membrane protein 7 isoform X1 [KO:K08515]
120913664  IDS; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
120913753  LAMP2; lysosome-associated membrane glycoprotein 2 isoform X1 [KO:K06528]
120913868  SLC2A6; solute carrier family 2, facilitated glucose transporter member 6 [KO:K08144]
120913914  TFE3; transcription factor E3 isoform X1 [KO:K09105]
120913928  ATP6AP1; V-type proton ATPase subunit S1 [KO:K03662]
120913975  IDUA; alpha-L-iduronidase [KO:K01217] [EC:3.2.1.76]
120914035  ABCA2; ATP-binding cassette sub-family A member 2 isoform X1 [KO:K05642]
120914568  HGSNAT; heparan-alpha-glucosaminide N-acetyltransferase isoform X1 [KO:K10532] [EC:2.3.1.78]
120915165  VPS11; vacuolar protein sorting-associated protein 11 homolog [KO:K20179]
120915620  AP5B1; AP-5 complex subunit beta-1 [KO:K19022]
120915650  MTOR; serine/threonine-protein kinase mTOR isoform X1 [KO:K07203] [EC:2.7.11.1]
120915665  VPS26B; vacuolar protein sorting-associated protein 26B [KO:K18466]
120916070  [KO:K02151]
120916512  AKT1S1; proline-rich AKT1 substrate 1 [KO:K16184]
120916518  [KO:K01379] [EC:3.4.23.5]
120916531  [KO:K11824]
120916889  SCARB2; lysosome membrane protein 2 isoform X1 [KO:K12384]
120917046  OSBPL5; oxysterol-binding protein-related protein 5 isoform X1 [KO:K20464]
120917112  TPCN2; two pore calcium channel protein 2 [KO:K14077]
120917139  ACP2; lysosomal acid phosphatase [KO:K14410] [EC:3.1.3.2]
120917294  [KO:K01379] [EC:3.4.23.5]
120917295  [KO:K01379] [EC:3.4.23.5]
120917307  [KO:K11824]
120917310  LAMTOR3; ragulator complex protein LAMTOR3 [KO:K04370]
120917468  PLA2G15; LOW QUALITY PROTEIN: phospholipase A2 group XV [KO:K06129] [EC:3.1.1.5]
120917498  CTSF; cathepsin F [KO:K01373] [EC:3.4.22.41]
120917525  SLC29A2; equilibrative nucleoside transporter 2 isoform X1 [KO:K15014]
120917542  [KO:K08569] [EC:3.4.22.-]
120917543  [KO:K08569] [EC:3.4.22.-]
120917631  [KO:K02146]
120917806  MEAK7; MTOR-associated protein MEAK7 [KO:K27947]
120917879  VPS35; vacuolar protein sorting-associated protein 35 [KO:K18468]
120917919  GALNS; N-acetylgalactosamine-6-sulfatase [KO:K01132] [EC:3.1.6.4]
120917937  AP1G1; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
120918214  CTSZ; cathepsin Z [KO:K08568] [EC:3.4.18.1]
120918258  NAGLU; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
120918357  MANBA; beta-mannosidase isoform X1 [KO:K01192] [EC:3.2.1.25]
120918572  [KO:K13289] [EC:3.4.16.5]
120918573  [KO:K13289] [EC:3.4.16.5]
120918779  TTI1; TELO2-interacting protein 1 homolog [KO:K20403]
120918847  ARSG; arylsulfatase G [KO:K12381] [EC:3.1.6.-]
120918878  MFSD8; major facilitator superfamily domain-containing protein 8 [KO:K12307]
120918944  PLEKHM1; pleckstrin homology domain-containing family M member 1 isoform X1 [KO:K23282]
120919005  RPTOR; regulatory-associated protein of mTOR [KO:K07204]
120919045  ATP6V0A1; V-type proton ATPase 116 kDa subunit a1 isoform X1 [KO:K02154]
120919064  ABCA5; ATP-binding cassette sub-family A member 5 [KO:K05648]
120919155  [KO:K12316] [EC:3.2.1.20]
120919158  OSBPL2; oxysterol-binding protein-related protein 2 [KO:K20174]
120919168  GGA3; ADP-ribosylation factor-binding protein GGA3 [KO:K12404]
120919333  [KO:K12316] [EC:3.2.1.20]
120919454  [KO:K20402]
120919573  SGSH; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
120920090  [KO:K01368] [EC:3.4.22.27]
120920158  [KO:K01368] [EC:3.4.22.27]
120920159  [KO:K01368] [EC:3.4.22.27]
120920237  CTSO; cathepsin O isoform X1 [KO:K01374] [EC:3.4.22.42]
120920254  LAMTOR2; ragulator complex protein LAMTOR2 [KO:K20398]
120920286  TMEM251; transmembrane protein 251 [KO:K26747]
120920305  GALC; galactocerebrosidase [KO:K01202] [EC:3.2.1.46]
120920357  [KO:K01368] [EC:3.4.22.27]
120920434  ZFYVE26; zinc finger FYVE domain-containing protein 26 isoform X1 [KO:K19027]
120920449  AP5M1; AP-5 complex subunit mu-1 [KO:K19023]
120920710  NPC2; NPC intracellular cholesterol transporter 2 [KO:K13443]
120920824  VPS39; vam6/Vps39-like protein [KO:K20183]
120920858  [KO:K02145] [EC:7.1.2.2]
120920961  LGMN; legumain [KO:K01369] [EC:3.4.22.34]
120920962  VPS18; vacuolar protein sorting-associated protein 18 homolog [KO:K20181]
120921003  AP4S1; AP-4 complex subunit sigma-1 [KO:K12403]
120921060  [KO:K01371] [EC:3.4.22.38]
120921061  [KO:K01371] [EC:3.4.22.38]
120921113  AGA; N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase [KO:K01444] [EC:3.5.1.26]
120921194  ATP6V1D; V-type proton ATPase subunit D [KO:K02149]
120921195  SNAPIN; SNARE-associated protein Snapin [KO:K20002]
120921849  TLR3; toll-like receptor 3 [KO:K05401]
120921971  ASAH1; acid ceramidase [KO:K12348] [EC:3.5.1.23]
120921993  [KO:K13443]
120923272  LAMTOR1; ragulator complex protein LAMTOR1 [KO:K20397]
120924554  ATP6V1B1; V-type proton ATPase subunit B, kidney isoform [KO:K02147]
120924594  AP5S1; AP-5 complex subunit sigma-1 [KO:K19024]
120926387  LAMP1; lysosome-associated membrane glycoprotein 1 [KO:K06528]
120926525  [KO:K05404]
120926526  [KO:K10170]
120926640  GUSB; beta-glucuronidase [KO:K01195] [EC:3.2.1.31]
120926690  [KO:K11825]
120926765  CLTC; clathrin heavy chain 1 isoform X1 [KO:K04646]
120926781  PPT1; palmitoyl-protein thioesterase 1 [KO:K01074] [EC:3.1.2.22]
120926788  FUCA1; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
120926898  RRAGC; ras-related GTP-binding protein C [KO:K16186]
120926947  LAPTM5; lysosomal-associated transmembrane protein 5 [KO:K12387]
120927030  [KO:K18467]
120927036  AP4B1; AP-4 complex subunit beta-1 isoform X1 [KO:K12401]
120927038  WDR7; WD repeat-containing protein 7 isoform X1 [KO:K24738]
120927137  LAMTOR5; ragulator complex protein LAMTOR5 [KO:K16344]
120927148  CTSE; cathepsin E isoform X1 [KO:K01382] [EC:3.4.23.34]
120927169  SORT1; sortilin [KO:K12388]
120927175  TFEB; transcription factor EB isoform X1 [KO:K15590]
120927614  NAGPA; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
120927749  CTNS; cystinosin isoform X1 [KO:K12386]
120928065  ATP6V1A; V-type proton ATPase catalytic subunit A [KO:K02145] [EC:7.1.2.2]
120928358  SLC38A9; sodium-coupled neutral amino acid transporter 9 [KO:K14995]
120928788  SMPD1; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
120928863  TPP1; tripeptidyl-peptidase 1 [KO:K01279] [EC:3.4.14.9]
120928963  CTSC; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
120928982  SLC36A4; proton-coupled amino acid transporter 4 isoform X1 [KO:K14209]
120929350  [KO:K01135] [EC:3.1.6.12]
120929397  AP3B1; AP-3 complex subunit beta-1 isoform X1 [KO:K12397]
120929429  SLC11A2; natural resistance-associated macrophage protein 2 isoform X1 [KO:K21398]
120929555  CD63; CD63 antigen [KO:K06497]
120929557  BLOC1S1; biogenesis of lysosome-related organelles complex 1 subunit 1 isoform X1 [KO:K20185]
120929694  CLN5; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
120929744  [KO:K12373] [EC:3.2.1.52]
120929770  HEXB; beta-hexosaminidase subunit beta isoform X1 [KO:K12373] [EC:3.2.1.52]
120930385  [KO:K01382] [EC:3.4.23.34]
120930947  LAMTOR4; ragulator complex protein LAMTOR4 [KO:K20399]
120931078  SPG11; spatacsin [KO:K19026]
120931093  CLN6; ceroid-lipofuscinosis neuronal protein 6 [KO:K12359]
120931216  [KO:K12399]
120931312  BLOC1S6; biogenesis of lysosome-related organelles complex 1 subunit 6 [KO:K20188]
120931336  DMXL2; dmX-like protein 2 isoform X1 [KO:K24155]
120931343  AP4E1; AP-4 complex subunit epsilon-1 isoform X1 [KO:K12400]
120931432  [KO:K01365] [EC:3.4.22.15]
120931433  [KO:K01365] [EC:3.4.22.15]
120931434  [KO:K01365] [EC:3.4.22.15]
120931450  AP3B2; AP-3 complex subunit beta-2 isoform X1 [KO:K12397]
120931517  VPS13C; vacuolar protein sorting-associated protein 13C [KO:K19525]
120931563  [KO:K01365] [EC:3.4.22.15]
120931568  ARSA; arylsulfatase A isoform X1 [KO:K01134] [EC:3.1.6.8]
120931617  ATP6V1F; V-type proton ATPase subunit F [KO:K02151]
120931836  [KO:K07955]
120931837  [KO:K01197] [EC:3.2.1.35]
120931843  [KO:K03662]
120931886  AP3S1; AP-3 complex subunit sigma-1 isoform X1 [KO:K12399]
120931958  DMXL1; dmX-like protein 1 isoform X1 [KO:K24155]
120932008  GNS; N-acetylglucosamine-6-sulfatase [KO:K01137] [EC:3.1.6.14]
120932134  GNPTAB; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
120932179  CLTB; clathrin light chain B isoform X1 [KO:K04645]
120932276  ATP6V0E1; V-type proton ATPase subunit e 1 [KO:K02153]
120932521  [KO:K07955]
120932615  [KO:K14209]
120932616  [KO:K12383]
120932617  [KO:K12383]
120932619  [KO:K12383]
120932719  ATP6V1E1; V-type proton ATPase subunit E 1 [KO:K02150]
120932731  BORCS5; BLOC-1-related complex subunit 5 [KO:K20819]
120932747  ATP6V0A4; V-type proton ATPase 116 kDa subunit a [KO:K02154]
120933028  VAMP8; vesicle-associated membrane protein 8 [KO:K08512]
120933083  ENTPD4; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
120933121  ATP6V1B2; V-type proton ATPase subunit B, brain isoform [KO:K02147]
120933162  AP3M2; AP-3 complex subunit mu-2 [KO:K12398]
120933207  MCOLN1; mucolipin-1 [KO:K04992]
120933298  AP1M2; AP-1 complex subunit mu-2 [KO:K12393]
120933339  ACP5; tartrate-resistant acid phosphatase type 5 isoform X1 [KO:K14379] [EC:3.1.3.2]
120933354  DNASE2; deoxyribonuclease-2-alpha isoform X1 [KO:K01158] [EC:3.1.22.1]
120933374  MAN2B1; lysosomal alpha-mannosidase [KO:K12311] [EC:3.2.1.24]
120933433  VPS29; vacuolar protein sorting-associated protein 29 isoform X1 [KO:K18467]
120933480  AP1S1; AP-1 complex subunit sigma-1A [KO:K12394]
120933514  AP4M1; AP-4 complex subunit mu-1 [KO:K12402]
120933785  VPS33A; vacuolar protein sorting-associated protein 33A [KO:K20182]
120934180  [KO:K01135] [EC:3.1.6.12]
120934481  ABCB9; ATP-binding cassette sub-family B member 9 [KO:K05656]
120934673  ATP6V0A2; V-type proton ATPase 116 kDa subunit a2 [KO:K02154]
120935695  CLN8; protein CLN8 [KO:K12360]
120936191  CTSB; cathepsin B [KO:K01363] [EC:3.4.22.1]
120936271  SNAP29; synaptosomal-associated protein 29 [KO:K08509]
120936292  CLTCL1; clathrin heavy chain 2 isoform X1 [KO:K04646]
120936301  LAPTM4A; lysosomal-associated transmembrane protein 4A [KO:K12387]
120936338  ATP6V1C2; V-type proton ATPase subunit C 2 [KO:K02148]
120936570  AP1S3; AP-1 complex subunit sigma-3 [KO:K12395]
120936796  LAMP3; lysosome-associated membrane glycoprotein 3 isoform X1 [KO:K06562]
120936932  AP2M1; AP-2 complex subunit mu isoform X1 [KO:K11826]
120936946  [KO:K12307]
120937036  SLC17A5; sialin [KO:K12301]
120937113  RRAGD; ras-related GTP-binding protein D isoform X1 [KO:K16186]
120937185  OSTM1; osteopetrosis-associated transmembrane protein 1 [KO:K23863]
120937197  CD164; sialomucin core protein 24 [KO:K06546]
120937202  FIG4; polyphosphoinositide phosphatase [KO:K22913] [EC:3.1.3.-]
120937292  NCOA7; nuclear receptor coactivator 7 isoform X1 [KO:K25442]
120937387  FUCA2; plasma alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
120937585  IGF2R; cation-independent mannose-6-phosphate receptor [KO:K06564]
120938008  [KO:K12387]
120938048  LAMP5; lysosome-associated membrane glycoprotein 5 [KO:K28774]
120938090  SLC29A1; equilibrative nucleoside transporter 1 [KO:K15014]
120938949  TPCN1; two pore calcium channel protein 1 [KO:K16896]
120939359  AP1B1; AP-1 complex subunit beta-1 isoform X1 [KO:K12392]
120940188  OSBPL3; oxysterol-binding protein-related protein 3 isoform X1 [KO:K20463]
120940380  VPS41; vacuolar protein sorting-associated protein 41 homolog [KO:K20184]
120940460  GLB1; beta-galactosidase [KO:K12309] [EC:3.2.1.23]
120940464  STX17; syntaxin-17 [KO:K08491]
120940701  BLOC1S5; biogenesis of lysosome-related organelles complex 1 subunit 5 [KO:K20187]
120940736  DTNBP1; dysbindin [KO:K20189]
120940787  BLOC1S4; biogenesis of lysosome-related organelles complex 1 subunit 4 [KO:K08366]
120940925  NPC1; NPC intracellular cholesterol transporter 1 [KO:K12385]
120940930  OSBPL1A; oxysterol-binding protein-related protein 1 isoform X1 [KO:K20174]
120940974  [KO:K05016]
120940990  ATP6V1H; V-type proton ATPase subunit H isoform X1 [KO:K02144]
120941002  SLC15A4; solute carrier family 15 member 4 [KO:K14638]
120941127  AP1G2; AP-1 complex subunit gamma-like 2 isoform X1 [KO:K12391]
120941258  ATP6V0D2; V-type proton ATPase subunit d 2 [KO:K02146]
120941407  LAPTM4B; lysosomal-associated transmembrane protein 4B [KO:K12387]
120941439  ATP6V1C1; V-type proton ATPase subunit C 1 [KO:K02148]
120941500  DEPTOR; DEP domain-containing mTOR-interacting protein [KO:K20402]
120941746  AP5Z1; AP-5 complex subunit zeta-1 [KO:K19025]
120942021  [KO:K01365] [EC:3.4.22.15]
120942037  [KO:K01365] [EC:3.4.22.15]
120942916  VPS13A; vacuolar protein sorting-associated protein 13A isoform X1 [KO:K19525]
120943084  CLN3; battenin [KO:K12389]
120943210  CLCN7; H(+)/Cl(-) exchange transporter 7 [KO:K05016]
120943218  ROGDI; protein rogdi homolog isoform X1 [KO:K24628]
120943286  MLST8; target of rapamycin complex subunit LST8 [KO:K08266]
120943350  TELO2; telomere length regulation protein TEL2 homolog isoform X1 [KO:K11137]
120943367  ATP6V0C; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
120943436  GNPTG; N-acetylglucosamine-1-phosphotransferase subunit gamma [KO:K10087]
120943521  NAGA; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
120943594  [KO:K19363]
120943596  [KO:K19363]
120943675  VPS16; vacuolar protein sorting-associated protein 16 homolog isoform X1 [KO:K20180]
120943775  [KO:K00921] [EC:2.7.1.150]
120943963  OSBPL6; oxysterol-binding protein-related protein 6 isoform X1 [KO:K20463]
120943995  GPR155; integral membrane protein GPR155 isoform X1 [KO:K28455]
120944222  SLC11A1; natural resistance-associated macrophage protein 1 [KO:K12347]
120944289  [KO:K06497]
120944794  [KO:K01197] [EC:3.2.1.35]
120944795  [KO:K01197] [EC:3.2.1.35]
120944893  ARL8B; ADP-ribosylation factor-like protein 8B [KO:K07955]
120944901  SUMF1; formylglycine-generating enzyme [KO:K13444] [EC:1.8.3.7]
120944967  [KO:K01197] [EC:3.2.1.35]
120944968  [KO:K01197] [EC:3.2.1.35]
120944969  [KO:K01197] [EC:3.2.1.35]
120944970  [KO:K01197] [EC:3.2.1.35]
120944982  [KO:K05404]
120945011  GGA1; ADP-ribosylation factor-binding protein GGA1 [KO:K12404]
120945095  RAB7A; ras-related protein Rab-7a [KO:K07897]
120945169  MITF; microphthalmia-associated transcription factor isoform X1 [KO:K09455]
120945590  ATP6V1G3; V-type proton ATPase subunit G 3 [KO:K02152]
120945966  MCOLN3; mucolipin-3 isoform X1 [KO:K04994]
120945968  MCOLN2; mucolipin-2 isoform X1 [KO:K04993]
120945979  DNASE2B; deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
120945990  [KO:K05404]
120946149  ATP6V0B; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
120946677  [KO:K02153]
120946927  M6PR; cation-dependent mannose-6-phosphate receptor [KO:K10089]
120946948  CLTA; clathrin light chain A isoform X1 [KO:K04644]
120946989  BORCS7; BLOC-1-related complex subunit 7 [KO:K20821]
120947097  [KO:K01052] [EC:3.1.1.13]
120947099  [KO:K01052] [EC:3.1.1.13]
120947144  BLOC1S2; biogenesis of lysosome-related organelles complex 1 subunit 2 [KO:K16750]
120947150  VPS26A; vacuolar protein sorting-associated protein 26A [KO:K18466]
Compound
C00002  ATP
C00008  ADP
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)
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Related
pathway
rtem00511  Other glycan degradation
rtem00531  Glycosaminoglycan degradation
rtem04130  SNARE interactions in vesicular transport
rtem04140  Autophagy - animal
rtem04144  Endocytosis
rtem04145  Phagosome
rtem04150  mTOR signaling pathway
rtem04620  Toll-like receptor signaling pathway
KO pathway
ko04142   

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