KEGG   PATHWAY: pcad04141
Entry
pcad04141                   Pathway                                
Name
Protein processing in endoplasmic reticulum - Physeter macrocephalus (sperm whale)
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
pcad04141  Protein processing in endoplasmic reticulum
pcad04141

Other DBs
GO: 0030433 0034976
Organism
Physeter macrocephalus (sperm whale) [GN:pcad]
Gene
102973242  RAD23A; UV excision repair protein RAD23 homolog A isoform X1 [KO:K10839]
102973351  MOGS; mannosyl-oligosaccharide glucosidase [KO:K01228] [EC:3.2.1.106]
102973353  PDIA6; protein disulfide-isomerase A6 isoform X1 [KO:K09584] [EC:5.3.4.1]
102973375  [KO:K03283]
102973409  STT3B; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B [KO:K07151] [EC:2.4.99.18]
102973475  BAG1; BAG family molecular chaperone regulator 1 [KO:K09555]
102973635  UBXN6; UBX domain-containing protein 6 [KO:K14011]
102974192  SSR3; translocon-associated protein subunit gamma [KO:K13251]
102974205  UBXN1; UBX domain-containing protein 1 isoform X1 [KO:K24348]
102974236  UBXN8; UBX domain-containing protein 8 isoform X1 [KO:K24351]
102974358  [KO:K03283]
102974380  YOD1; ubiquitin thioesterase OTU1 [KO:K13719] [EC:3.1.2.-]
102974828  DNAJC5; dnaJ homolog subfamily C member 5 isoform X1 [KO:K09525]
102975353  UBE4B; ubiquitin conjugation factor E4 B isoform X4 [KO:K10597] [EC:2.3.2.27]
102975469  PPP1R15A; LOW QUALITY PROTEIN: protein phosphatase 1 regulatory subunit 15A [KO:K14019]
102975641  DNAJC5G; LOW QUALITY PROTEIN: dnaJ homolog subfamily C member 5G [KO:K09525]
102975879  SYVN1; E3 ubiquitin-protein ligase synoviolin [KO:K10601] [EC:2.3.2.27]
102975945  DNAJA2; dnaJ homolog subfamily A member 2 [KO:K09503]
102975968  EIF2S1; eukaryotic translation initiation factor 2 subunit 1 [KO:K03237]
102976041  CAPN2; calpain-2 catalytic subunit isoform X1 [KO:K03853] [EC:3.4.22.53]
102976058  SSR4; translocon-associated protein subunit delta isoform X4 [KO:K04571]
102976135  TRAM1; translocating chain-associated membrane protein 1 [KO:K14010]
102976214  AMFR; E3 ubiquitin-protein ligase AMFR [KO:K10636] [EC:2.3.2.36]
102976232  DNAJB1; dnaJ homolog subfamily B member 1 [KO:K09507]
102976357  RNF5; E3 ubiquitin-protein ligase RNF5 isoform X1 [KO:K10666] [EC:2.3.2.27]
102976379  UBQLN3; ubiquilin-3 [KO:K04523]
102976449  SEC24C; protein transport protein Sec24C isoform X2 [KO:K14007]
102976852  [KO:K08057]
102976909  MAP3K5; mitogen-activated protein kinase kinase kinase 5 isoform X1 [KO:K04426] [EC:2.7.11.25]
102977083  LMAN1; protein ERGIC-53 [KO:K10080]
102977417  MAPK9; mitogen-activated protein kinase 9 isoform X1 [KO:K04440] [EC:2.7.11.24]
102977644  RPN1; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 [KO:K12666]
102977684  MAGT1; magnesium transporter protein 1 isoform X2 [KO:K19478]
102978131  ATF6B; LOW QUALITY PROTEIN: cyclic AMP-dependent transcription factor ATF-6 beta [KO:K09049]
102978248  DNAJC10; dnaJ homolog subfamily C member 10 isoform X1 [KO:K09530] [EC:1.8.4.-]
102978295  HSPA4L; heat shock 70 kDa protein 4L [KO:K09485]
102978313  SEC63; translocation protein SEC63 homolog isoform X1 [KO:K09540]
102978373  UBQLN4; ubiquilin-4 [KO:K04523]
102978403  [KO:K04079]
102978657  DERL3; derlin-3 isoform X2 [KO:K13989]
102978674  SSR2; translocon-associated protein subunit beta [KO:K13250]
102978806  RRBP1; ribosome-binding protein 1 [KO:K14000]
102978868  STUB1; E3 ubiquitin-protein ligase CHIP [KO:K09561] [EC:2.3.2.27]
102978958  SEC61A1; protein transport protein Sec61 subunit alpha [KO:K10956]
102979169  NSFL1C; NSFL1 cofactor p47 isoform X2 [KO:K14012]
102979589  SEC31A; protein transport protein Sec31A isoform X1 [KO:K14005]
102979645  UBE2G2; ubiquitin-conjugating enzyme E2 G2 isoform X1 [KO:K04555] [EC:2.3.2.23]
102979652  DDIT3; DNA damage-inducible transcript 3 protein [KO:K04452]
102979658  SEC13; protein SEC13 homolog [KO:K14004]
102979763  [KO:K08288]
102979796  PDIA3; protein disulfide-isomerase A3 [KO:K08056] [EC:5.3.4.1]
102979882  ERO1B; ERO1-like protein beta isoform X4 [KO:K10976] [EC:1.8.4.-]
102979961  SEC24A; protein transport protein Sec24A isoform X1 [KO:K14007]
102980083  [KO:K04079]
102980242  [KO:K04452]
102980316  OSTC; oligosaccharyltransferase complex subunit OSTC isoform X1 [KO:K26501]
102980323  UBE2D2; ubiquitin-conjugating enzyme E2 D2 isoform X2 [KO:K06689] [EC:2.3.2.23]
102980440  [KO:K03094]
102980452  SAR1B; GTP-binding protein SAR1b [KO:K07953] [EC:3.6.5.-]
102980465  SIL1; nucleotide exchange factor SIL1 isoform X1 [KO:K14001]
102980473  UBE2J2; ubiquitin-conjugating enzyme E2 J2 [KO:K04554] [EC:2.3.2.23]
102980856  SEC23B; protein transport protein Sec23B [KO:K14006]
102981325  DNAJA1; dnaJ homolog subfamily A member 1 [KO:K09502]
102981655  NGLY1; peptide-N(4)-(N-acetyl-beta- glucosaminyl)asparagine amidase isoform X2 [KO:K01456] [EC:3.5.1.52]
102981822  EIF2AK3; eukaryotic translation initiation factor 2-alpha kinase 3 isoform X1 [KO:K08860] [EC:2.7.11.1]
102981992  DNAJB2; dnaJ homolog subfamily B member 2 isoform X1 [KO:K09508]
102982022  PRKN; E3 ubiquitin-protein ligase parkin isoform X1 [KO:K04556] [EC:2.3.2.31]
102982026  SEC24D; protein transport protein Sec24D isoform X1 [KO:K14007]
102982384  [KO:K03094]
102982464  SEC61B; protein transport protein Sec61 subunit beta [KO:K09481]
102982689  HSPA8; LOW QUALITY PROTEIN: heat shock cognate 71 kDa protein [KO:K03283]
102982702  [KO:K03094]
102982870  UGGT1; UDP-glucose:glycoprotein glucosyltransferase 1 isoform X1 [KO:K11718] [EC:2.4.1.-]
102982982  MAN1A1; mannosyl-oligosaccharide 1,2-alpha-mannosidase IA [KO:K01230] [EC:3.2.1.113]
102983086  UBXN2A; UBX domain-containing protein 2A isoform X1 [KO:K24349]
102983244  CRYAA; alpha-crystallin A chain [KO:K09541]
102983292  ATF6; cyclic AMP-dependent transcription factor ATF-6 alpha isoform X3 [KO:K09054]
102983370  [KO:K03094]
102983408  SAR1A; GTP-binding protein SAR1a [KO:K07953] [EC:3.6.5.-]
102983502  HSPBP1; hsp70-binding protein 1 [KO:K09562]
102983511  BCAP31; B-cell receptor-associated protein 31 [KO:K14009]
102983768  HSPA5; endoplasmic reticulum chaperone BiP [KO:K09490] [EC:3.6.4.10]
102983779  CKAP4; cytoskeleton-associated protein 4 [KO:K13999]
102983803  [KO:K03283]
102983921  VCP; transitional endoplasmic reticulum ATPase [KO:K13525]
102983945  UBE2D3; ubiquitin-conjugating enzyme E2 D3 isoform X1 [KO:K06689] [EC:2.3.2.23]
102984157  ATF4; cyclic AMP-dependent transcription factor ATF-4 [KO:K04374]
102984173  [KO:K03347]
102984214  EDEM1; ER degradation-enhancing alpha-mannosidase-like protein 1 [KO:K10084]
102984328  SEC24B; protein transport protein Sec24B isoform X1 [KO:K14007]
102984376  P4HB; protein disulfide-isomerase [KO:K09580] [EC:5.3.4.1]
102984407  CANX; calnexin [KO:K08054]
102984504  CAPN1; calpain-1 catalytic subunit isoform X1 [KO:K01367] [EC:3.4.22.52]
102984741  MAPK10; mitogen-activated protein kinase 10 [KO:K04440] [EC:2.7.11.24]
102984850  [KO:K07765] [EC:3.4.24.85]
102984914  SELENOS; selenoprotein S isoform X1 [KO:K14025]
102984973  UBQLN1; ubiquilin-1 isoform X1 [KO:K04523]
102985047  HSP90AB1; heat shock protein HSP 90-beta [KO:K04079]
102985100  TXNDC5; thioredoxin domain-containing protein 5 [KO:K13984] [EC:5.3.4.1]
102985209  UBE2G1; ubiquitin-conjugating enzyme E2 G1 [KO:K10575] [EC:2.3.2.23]
102985279  WFS1; wolframin [KO:K14020]
102985576  XBP1; LOW QUALITY PROTEIN: X-box-binding protein 1 [KO:K09027]
102985963  ATXN3; ataxin-3 isoform X1 [KO:K11863] [EC:3.4.22.-]
102985990  HSPH1; heat shock protein 105 kDa isoform X2 [KO:K09485]
102986039  BAG2; BAG family molecular chaperone regulator 2 [KO:K09556]
102986227  [KO:K03283]
102986386  OS9; protein OS-9 isoform X1 [KO:K10088]
102986445  UGGT2; UDP-glucose:glycoprotein glucosyltransferase 2 isoform X1 [KO:K11718] [EC:2.4.1.-]
102986454  [KO:K10575] [EC:2.3.2.23]
102986611  RPN2; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 isoform X2 [KO:K12667]
102986700  LMAN2; vesicular integral-membrane protein VIP36 isoform X1 [KO:K10082]
102986724  DNAJC3; dnaJ homolog subfamily C member 3 isoform X1 [KO:K09523]
102987023  SEC61A2; protein transport protein Sec61 subunit alpha isoform X1 [KO:K10956]
102987289  NPLOC4; nuclear protein localization protein 4 homolog isoform X3 [KO:K14015]
102987621  ERO1A; ERO1-like protein alpha isoform X2 [KO:K10950] [EC:1.8.4.-]
102987670  [KO:K08852] [EC:2.7.11.1 3.1.26.-]
102987703  DNAJC5B; dnaJ homolog subfamily C member 5B isoform X1 [KO:K09525]
102987730  SSR1; translocon-associated protein subunit alpha [KO:K13249]
102987847  [KO:K23741]
102987942  BCL2; apoptosis regulator Bcl-2 isoform X1 [KO:K02161]
102988042  ERLEC1; endoplasmic reticulum lectin 1 isoform X1 [KO:K14008]
102988230  STT3A; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A isoform X2 [KO:K07151] [EC:2.4.99.18]
102988249  UBXN4; UBX domain-containing protein 4 isoform X1 [KO:K24348]
102988360  [KO:K09502]
102988570  HSP90AA1; heat shock protein HSP 90-alpha [KO:K04079]
102988591  DNAJB12; dnaJ homolog subfamily B member 12 [KO:K09518]
102988702  FBXO6; F-box only protein 6 isoform X3 [KO:K10100]
102988730  DNAJC1; dnaJ homolog subfamily C member 1 [KO:K09521]
102988796  KRTCAP2; LOW QUALITY PROTEIN: keratinocyte-associated protein 2 [KO:K28202]
102988995  TRAM1L1; translocating chain-associated membrane protein 1-like 1 [KO:K14010]
102989018  DNAJB11; dnaJ homolog subfamily B member 11 [KO:K09517]
102989030  [KO:K03283]
102989215  UFD1; ubiquitin recognition factor in ER-associated degradation protein 1 isoform X2 [KO:K14016]
102989276  PREB; prolactin regulatory element-binding protein isoform X1 [KO:K14003]
102989406  LMAN1L; protein ERGIC-53-like [KO:K10081]
102989734  RNF185; E3 ubiquitin-protein ligase RNF185 [KO:K10666] [EC:2.3.2.27]
102989763  SEC23A; protein transport protein Sec23A [KO:K14006]
102989809  TMEM258; transmembrane protein 258 [KO:K26502]
102989901  [KO:K03868] [EC:2.3.2.32]
102990063  HYOU1; hypoxia up-regulated protein 1 isoform X1 [KO:K09486]
102990186  FBXO2; F-box only protein 2 [KO:K10099]
102990501  [KO:K26501]
102990601  HSPA6; LOW QUALITY PROTEIN: heat shock 70 kDa protein 6 [KO:K03283]
102990681  DERL2; derlin-2 isoform X1 [KO:K13989]
102990733  HSP90B1; endoplasmin [KO:K09487]
102991092  BAK1; bcl-2 homologous antagonist/killer [KO:K14021]
102991262  TUSC3; tumor suppressor candidate 3 isoform X2 [KO:K19478]
102991436  DAD1; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 [KO:K12668]
102991760  MAN1C1; mannosyl-oligosaccharide 1,2-alpha-mannosidase IC isoform X1 [KO:K01230] [EC:3.2.1.113]
102991774  MAP2K7; dual specificity mitogen-activated protein kinase kinase 7 isoform X3 [KO:K04431] [EC:2.7.12.2]
102991804  RAD23B; UV excision repair protein RAD23 homolog B isoform X1 [KO:K10839]
102992099  NFE2L2; nuclear factor erythroid 2-related factor 2 isoform X1 [KO:K05638]
102992328  SEL1L; protein sel-1 homolog 1 isoform X2 [KO:K14026]
102992388  PLAA; phospholipase A-2-activating protein [KO:K14018]
102992492  SEL1L2; protein sel-1 homolog 2 isoform X1 [KO:K14026]
102992972  ERP29; endoplasmic reticulum resident protein 29 [KO:K09586]
102993106  [KO:K08653] [EC:3.4.21.112]
102993328  SKP1; S-phase kinase-associated protein 1 [KO:K03094]
102993329  [KO:K06689] [EC:2.3.2.23]
102993338  SEC62; translocation protein SEC62 [KO:K12275]
102993376  UBE2J1; ubiquitin-conjugating enzyme E2 J1 [KO:K10578] [EC:2.3.2.23]
102993452  EDEM3; ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X1 [KO:K10086]
102993454  SEC31B; LOW QUALITY PROTEIN: protein transport protein Sec31B [KO:K14005]
102993460  PDIA4; protein disulfide-isomerase A4 [KO:K09582] [EC:5.3.4.1]
102993732  CUL1; LOW QUALITY PROTEIN: cullin-1 [KO:K03347]
102993912  DDOST; dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit [KO:K12670]
102993947  UBQLN2; ubiquilin-2 [KO:K04523]
102994182  SEC61G; protein transport protein Sec61 subunit gamma isoform X4 [KO:K07342]
102994512  MARCHF6; E3 ubiquitin-protein ligase MARCHF6 isoform X2 [KO:K10661] [EC:2.3.2.27]
102994900  CRYAB; alpha-crystallin B chain isoform X1 [KO:K09542]
102994908  [KO:K03283]
102995190  [KO:K03283]
102995465  [KO:K03283]
102996121  [KO:K10956]
102996185  TRAF2; TNF receptor-associated factor 2 isoform X1 [KO:K03173] [EC:2.3.2.27]
102996281  [KO:K07953] [EC:3.6.5.-]
102996353  MAPK8; mitogen-activated protein kinase 8 isoform X3 [KO:K04440] [EC:2.7.11.24]
102996366  GANAB; neutral alpha-glucosidase AB isoform X1 [KO:K05546] [EC:3.2.1.207]
102996462  HERPUD1; homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein [KO:K14027]
102996730  UBE2D1; LOW QUALITY PROTEIN: ubiquitin-conjugating enzyme E2 D1 [KO:K06689] [EC:2.3.2.23]
102996910  CALR; calreticulin [KO:K08057]
102996926  DERL1; derlin-1 [KO:K11519]
102996939  MAN1A2; mannosyl-oligosaccharide 1,2-alpha-mannosidase IB [KO:K01230] [EC:3.2.1.113]
112062207  [KO:K03347]
112063636  SVIP; small VCP/p97-interacting protein [KO:K14014]
112064697  [KO:K03868] [EC:2.3.2.32]
112065466  [KO:K07342]
112065486  [KO:K23741]
112067306  [KO:K04523]
114483867  MBTPS1; membrane-bound transcription factor site-1 protease [KO:K08653] [EC:3.4.21.112]
114485282  [KO:K14001]
129391321  EDEM2; ER degradation-enhancing alpha-mannosidase-like protein 2 [KO:K10085]
129391324  RBX1; E3 ubiquitin-protein ligase RBX1 isoform X1 [KO:K03868] [EC:2.3.2.32]
129391776  [KO:K07342]
129392741  [KO:K26501]
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
pcad00510  N-Glycan biosynthesis
pcad03050  Proteasome
pcad03060  Protein export
pcad04210  Apoptosis
pcad04930  Type II diabetes mellitus
pcad05010  Alzheimer disease
pcad05012  Parkinson disease
pcad05020  Prion disease
KO pathway
ko04141   

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