KEGG   PATHWAY: rtp04141
Entry
rtp04141                    Pathway                                
Name
Protein processing in endoplasmic reticulum - Rhincodon typus (whale shark)
Description
The endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylated. Correctly folded proteins are packaged into transport vesicles that shuttle them to the Golgi complex. Misfolded proteins are retained within the ER lumen in complex with molecular chaperones. Proteins that are terminally misfolded bind to BiP and are directed toward degradation through the proteasome in a process called ER-associated degradation (ERAD). Accumulation of misfolded proteins in the ER causes ER stress and activates a signaling pathway called the unfolded protein response (UPR). In certain severe situations, however, the protective mechanisms activated by the UPR are not sufficient to restore normal ER function and cells die by apoptosis.
Class
Genetic Information Processing; Folding, sorting and degradation
Pathway map
rtp04141  Protein processing in endoplasmic reticulum
rtp04141

Other DBs
GO: 0030433 0034976
Organism
Rhincodon typus (whale shark) [GN:rtp]
Gene
109921354  protein transport protein Sec61 subunit alpha-like 1 [KO:K10956]
109929694  protein transport protein Sec61 subunit alpha isoform X1 [KO:K10956]
109911405  sec61b; protein transport protein Sec61 subunit beta [KO:K09481]
109913151  sec61g; protein transport protein Sec61 subunit gamma [KO:K07342]
109935744  sec62; translocation protein SEC62 [KO:K12275]
109929801  sec63; translocation protein SEC63 homolog [KO:K09540]
109917919  rpn1; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 [KO:K12666]
109923240  rpn2; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 isoform X1 [KO:K12667]
109934151  dad1; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 [KO:K12668]
109927778  ddost; dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit [KO:K12670]
109924687  stt3b; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B [KO:K07151] [EC:2.4.99.18]
109916501  stt3a; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A [KO:K07151] [EC:2.4.99.18]
109911320  magnesium transporter protein 1-like [KO:K19478]
109929479  tumor suppressor candidate 3 [KO:K19478]
109911532  ostc; oligosaccharyltransferase complex subunit ostc isoform X1 [KO:K26501]
109921165  tmem258; transmembrane protein 258 [KO:K26502]
109934039  mogs; mannosyl-oligosaccharide glucosidase [KO:K01228] [EC:3.2.1.106]
109915626  cytoskeleton-associated protein 4 isoform X1 [KO:K13999]
109910579  ribosome-binding protein 1 isoform X1 [KO:K14000]
109914872  sil1; nucleotide exchange factor SIL1 isoform X2 [KO:K14001]
109922561  hyou1; hypoxia up-regulated protein 1 [KO:K09486]
109913839  hspa5; endoplasmic reticulum chaperone BiP [KO:K09490] [EC:3.6.4.10]
109915057  dnajc3a; dnaJ homolog subfamily C member 3a isoform X1 [KO:K09523]
109917879  hsp90b1; endoplasmin [KO:K09487]
109925267  neutral alpha-glucosidase AB isoform X1 [KO:K05546] [EC:3.2.1.207]
109920560  prkcsh; glucosidase 2 subunit beta [KO:K08288]
109911595  si:ch211-274f20.2; calnexin isoform X1 [KO:K08054]
109915453  canx; calnexin [KO:K08054]
109926671  pdia3; protein disulfide-isomerase A3 [KO:K08056] [EC:5.3.4.1]
109928326  calreticulin-like isoform X1 [KO:K08057]
109927429  calreticulin-like [KO:K08057]
109913938  calreticulin [KO:K08057]
109928645  man1a1; mannosyl-oligosaccharide 1,2-alpha-mannosidase IA [KO:K01230] [EC:3.2.1.113]
109930822  mannosyl-oligosaccharide 1,2-alpha-mannosidase IA-like [KO:K01230] [EC:3.2.1.113]
109930719  man1a2; mannosyl-oligosaccharide 1,2-alpha-mannosidase IB isoform X1 [KO:K01230] [EC:3.2.1.113]
109927301  man1b1b; mannosidase, alpha, class 1B, member 1b isoform X1 [KO:K23741] [EC:3.2.1.209]
109917286  lman1; protein ERGIC-53 [KO:K10080]
109922712  GTP-binding protein SAR1a [KO:K07953] [EC:3.6.5.-]
109926894  sar1b; GTP-binding protein SAR1b [KO:K07953] [EC:3.6.5.-]
109934953  sec13; protein SEC13 homolog [KO:K14004]
109915130  sec31b; protein transport protein Sec31A isoform X1 [KO:K14005]
109910901  protein transport protein Sec23B isoform X1 [KO:K14006]
109926764  sec23a; protein transport protein Sec23A [KO:K14006]
109931802  sec24b; protein transport protein Sec24B [KO:K14007]
109930123  sec24c; protein transport protein Sec24C [KO:K14007]
109937235  protein transport protein Sec24A-like [KO:K14007]
109920485  sec24d; protein transport protein Sec24D [KO:K14007]
109935899  uggt1; UDP-glucose:glycoprotein glucosyltransferase 1 isoform X2 [KO:K11718] [EC:2.4.1.-]
109937460  edem1; ER degradation-enhancing alpha-mannosidase-like protein 1 [KO:K10084]
109910942  ER degradation-enhancing alpha-mannosidase-like protein 2 [KO:K10085]
109929173  edem3; ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X1 [KO:K10086]
109917682  ER degradation-enhancing alpha-mannosidase-like protein 3 [KO:K10086]
109923893  p4hb; protein disulfide-isomerase [KO:K09580] [EC:5.3.4.1]
109919689  protein disulfide-isomerase A4 [KO:K09582] [EC:5.3.4.1]
109928555  pdia6; protein disulfide-isomerase A6 [KO:K09584] [EC:5.3.4.1]
109930598  endoplasmic reticulum resident protein 29 [KO:K09586]
109912467  ERO1-like protein alpha [KO:K10950] [EC:1.8.4.-]
109911360  ero1b; ERO1-like protein beta isoform X1 [KO:K10976] [EC:1.8.4.-]
109914747  erlec1; endoplasmic reticulum lectin 1 isoform X1 [KO:K14008]
109912229  ssr1; translocon-associated protein subunit alpha isoform X2 [KO:K13249]
109926422  ssr2; translocon-associated protein subunit beta [KO:K13250]
109920780  ssr3; translocon-associated protein subunit gamma [KO:K13251]
109926013  bcap31; B-cell receptor-associated protein 31 [KO:K14009]
109911528  translocating chain-associated membrane protein 1 [KO:K14010]
109927928  translocating chain-associated membrane protein 1-like 1 [KO:K14010]
109914629  derl1; derlin-1 [KO:K11519]
109910765  derlin-2-like isoform X1 [KO:K13989]
109916869  derl2; derlin-2 [KO:K13989]
109919180  ubxn4; UBX domain-containing protein 4 isoform X1 [KO:K24348]
109924423  ubxn1; UBX domain-containing protein 1 [KO:K24348]
109922121  ubxn6; UBX domain-containing protein 6 [KO:K14011]
109912576  NSFL1 cofactor p47 [KO:K14012]
109927012  transitional endoplasmic reticulum ATPase [KO:K13525]
109936777  nploc4; nuclear protein localization protein 4 homolog isoform X1 [KO:K14015]
109939112  ufd1l; ubiquitin recognition factor in ER-associated degradation protein 1 isoform X3 [KO:K14016]
109914616  heat shock cognate 71 kDa protein-like [KO:K03283]
109926956  heat shock cognate 71 kDa protein-like [KO:K03283]
109914620  heat shock 70 kDa protein [KO:K03283]
109935266  putative heat shock 70 kDa protein 7 [KO:K03283]
109926968  dnaJ homolog subfamily A member 1 [KO:K09502]
109918736  dnaja2a; dnaJ homolog subfamily A member 2a [KO:K09503]
109936999  dnaJ homolog subfamily B member 1 [KO:K09507]
109924958  dnajb12a; dnaJ homolog subfamily B member 12a [KO:K09518]
109936885  dnaJ homolog subfamily C member 5-like [KO:K09525]
109933384  dnaJ homolog subfamily C member 5 [KO:K09525]
109932303  dnaJ homolog subfamily C member 5-like [KO:K09525]
109935825  dnajc5ga; dnaJ (Hsp40) homolog, subfamily C, member 5 gamma a [KO:K09525]
109921310  hsp90ab1; heat shock protein HSP 90-beta [KO:K04079]
109936404  heat shock protein HSP 90-alpha [KO:K04079]
109934435  heat shock protein 105 kDa isoform X1 [KO:K09485]
109928790  heat shock 70 kDa protein 4L [KO:K09485]
109917958  bag1; BAG family molecular chaperone regulator 1 [KO:K09555]
109928150  bag2; BAG family molecular chaperone regulator 2 [KO:K09556]
109932365  hsp70-binding protein 1 [KO:K09562]
109930998  cryabb; crystallin, alpha B, b isoform X1 [KO:K09542]
109927163  yod1; ubiquitin thioesterase OTU1 [KO:K13719] [EC:3.1.2.-]
109910926  plaa; phospholipase A-2-activating protein isoform X2 [KO:K14018]
109927430  UV excision repair protein RAD23 homolog B-like isoform X1 [KO:K10839]
109913939  UV excision repair protein RAD23 homolog A isoform X2 [KO:K10839]
109932528  ubiquilin-1 [KO:K04523]
109927533  ngly1; peptide-N(4)-(N-acetyl-beta- glucosaminyl)asparagine amidase [KO:K01456] [EC:3.5.1.52]
109934968  atxn3; ataxin-3 [KO:K11863] [EC:3.4.22.-]
109928820  eif2ak3; eukaryotic translation initiation factor 2-alpha kinase 3 isoform X1 [KO:K08860] [EC:2.7.11.1]
109933548  eif2s1b; eukaryotic translation initiation factor 2 subunit 1 [KO:K03237]
109910768  nfe2l2a; nuclear factor erythroid 2-related factor 2a isoform X1 [KO:K05638]
109919490  atf4a; cyclic AMP-dependent transcription factor ATF-4 [KO:K04374]
109930204  apoptosis regulator Bcl-2-like isoform X2 [KO:K02161]
109914523  mbtps1; membrane-bound transcription factor site-1 protease isoform X1 [KO:K08653] [EC:3.4.21.112]
109931902  mbtps2; membrane-bound transcription factor site-2 protease [KO:K07765] [EC:3.4.24.85]
109910482  ern2; serine/threonine-protein kinase/endoribonuclease IRE1 isoform X1 [KO:K08852] [EC:2.7.11.1 3.1.26.-]
109922055  TNF receptor-associated factor 2-like [KO:K03173] [EC:2.3.2.27]
109916783  traf2b; TNF receptor-associated factor 2 [KO:K03173] [EC:2.3.2.27]
109936083  TNF receptor-associated factor 2-like [KO:K03173] [EC:2.3.2.27]
109911816  map2k7; dual specificity mitogen-activated protein kinase kinase 7 [KO:K04431] [EC:2.7.12.2]
109927876  mapk10; mitogen-activated protein kinase 10 [KO:K04440] [EC:2.7.11.24]
109917844  mitogen-activated protein kinase 9 [KO:K04440] [EC:2.7.11.24]
109917855  mapk8a; mitogen-activated protein kinase 8 isoform X1 [KO:K04440] [EC:2.7.11.24]
109918844  zgc:153993; apoptosis regulator BAX [KO:K02159]
109917897  bcl-2 homologous antagonist/killer-like [KO:K14021]
109911651  bcl-2 homologous antagonist/killer isoform X3 [KO:K14021]
109928016  marchf6; E3 ubiquitin-protein ligase MARCH6 [KO:K10661] [EC:2.3.2.27]
109934796  ube2j1; ubiquitin-conjugating enzyme E2 J1 [KO:K10578] [EC:2.3.2.23]
109914836  ube2j2; ubiquitin-conjugating enzyme E2 J2 isoform X2 [KO:K04554] [EC:2.3.2.23]
109911397  ube2g1b; ubiquitin-conjugating enzyme E2G 1b [KO:K10575] [EC:2.3.2.23]
109915186  ube2g1a; ubiquitin-conjugating enzyme E2 G1 [KO:K10575] [EC:2.3.2.23]
109912213  ube2g2; ubiquitin-conjugating enzyme E2 G2 [KO:K04555] [EC:2.3.2.23]
109918486  syvn1; E3 ubiquitin-protein ligase synoviolin [KO:K10601] [EC:2.3.2.27]
109921112  rnf185; E3 ubiquitin-protein ligase RNF185 isoform X3 [KO:K10666] [EC:2.3.2.27]
109917004  selenos; selenoprotein S [KO:K14025]
109934240  protein sel-1 homolog 1 [KO:K14026]
109912816  sel1l; protein sel-1 homolog 1 [KO:K14026]
109927758  herpud1; homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein [KO:K14027]
109931938  amfra; autocrine motility factor receptor a [KO:K10636] [EC:2.3.2.36]
109935907  stub1; E3 ubiquitin-protein ligase CHIP isoform X2 [KO:K09561] [EC:2.3.2.27]
109937308  ubiquitin-conjugating enzyme E2 D2-like isoform X1 [KO:K06689] [EC:2.3.2.23]
109925499  ubiquitin-conjugating enzyme E2 D4-like isoform X1 [KO:K06689] [EC:2.3.2.23]
109912353  ube2d2; ubiquitin-conjugating enzyme E2 D2 isoform X1 [KO:K06689] [EC:2.3.2.23]
109916087  ube2d1b; ubiquitin-conjugating enzyme E2 D1b [KO:K06689] [EC:2.3.2.23]
109921792  rbx1; E3 ubiquitin-protein ligase RBX1 [KO:K03868] [EC:2.3.2.32]
109916300  cul1b; cullin-1b [KO:K03347]
109934365  S-phase kinase-associated protein 1-like isoform X1 [KO:K03094]
109912239  S-phase kinase-associated protein 1 [KO:K03094]
109918378  F-box only protein 2-like [KO:K10099]
Compound
C00076  Calcium cation
G00009   
G00010   
G00011   
G00012   
G10694   
Reference
PMID:19491040
  Authors
Naidoo N
  Title
ER and aging-Protein folding and the ER stress response.
  Journal
Ageing Res Rev 8:150-9 (2009)
DOI:10.1016/j.arr.2009.03.001
Reference
PMID:18023214
  Authors
Malhotra JD, Kaufman RJ
  Title
The endoplasmic reticulum and the unfolded protein response.
  Journal
Semin Cell Dev Biol 18:716-31 (2007)
DOI:10.1016/j.semcdb.2007.09.003
Reference
PMID:20347046
  Authors
Maattanen P, Gehring K, Bergeron JJ, Thomas DY
  Title
Protein quality control in the ER: the recognition of misfolded proteins.
  Journal
Semin Cell Dev Biol 21:500-11 (2010)
DOI:10.1016/j.semcdb.2010.03.006
Reference
PMID:20219571
  Authors
Stolz A, Wolf DH
  Title
Endoplasmic reticulum associated protein degradation: a chaperone assisted journey to hell.
  Journal
Biochim Biophys Acta 1803:694-705 (2010)
DOI:10.1016/j.bbamcr.2010.02.005
Reference
PMID:20112977
  Authors
Dejgaard K, Theberge JF, Heath-Engel H, Chevet E, Tremblay ML, Thomas DY
  Title
Organization of the Sec61 translocon, studied by high resolution native electrophoresis.
  Journal
J Proteome Res 9:1763-71 (2010)
DOI:10.1021/pr900900x
Related
pathway
rtp00510  N-Glycan biosynthesis
rtp03050  Proteasome
rtp03060  Protein export
rtp04210  Apoptosis
KO pathway
ko04141   
LinkDB

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