KEGG   PATHWAY: bom04141
Entry
bom04141                    Pathway                                
Name
Protein processing in endoplasmic reticulum - Bos mutus (wild yak)
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
bom04141  Protein processing in endoplasmic reticulum
bom04141

Other DBs
GO: 0030433 0034976
Organism
Bos mutus (wild yak) [GN:bom]
Gene
102264575  PPP1R15A; LOW QUALITY PROTEIN: protein phosphatase 1 regulatory subunit 15A [KO:K14019]
102264579  SEC24B; protein transport protein Sec24B isoform X1 [KO:K14007]
102264587  DNAJC1; dnaJ homolog subfamily C member 1 [KO:K09521]
102264640  SAR1B; small COPII coat GTPase SAR1B [KO:K07953] [EC:3.6.5.-]
102264895  HSPBP1; LOW QUALITY PROTEIN: hsp70-binding protein 1 [KO:K09562]
102264991  SEC61A1; protein transport protein Sec61 subunit alpha [KO:K10956]
102265217  LMAN1; LOW QUALITY PROTEIN: protein ERGIC-53 [KO:K10080]
102265458  NPLOC4; nuclear protein localization protein 4 homolog isoform X1 [KO:K14015]
102265463  STUB1; E3 ubiquitin-protein ligase CHIP [KO:K09561] [EC:2.3.2.27]
102265590  PDIA6; protein disulfide-isomerase A6 [KO:K09584] [EC:5.3.4.1]
102265668  ERP29; endoplasmic reticulum resident protein 29 [KO:K09586]
102265728  RNF5; E3 ubiquitin-protein ligase RNF5 [KO:K10666] [EC:2.3.2.27]
102265832  RPN1; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 [KO:K12666]
102266017  MAN1A2; mannosyl-oligosaccharide 1,2-alpha-mannosidase IB isoform X1 [KO:K01230] [EC:3.2.1.113]
102266177  OSTC; oligosaccharyltransferase complex subunit OSTC [KO:K26501]
102266347  SKP1; S-phase kinase-associated protein 1 [KO:K03094]
102266378  HYOU1; hypoxia up-regulated protein 1 isoform X1 [KO:K09486]
102266484  HSPH1; heat shock protein 105 kDa isoform X1 [KO:K09485]
102266544  BAK1; bcl-2 homologous antagonist/killer [KO:K14021]
102266729  UBXN8; UBX domain-containing protein 8 [KO:K24351]
102266912  [KO:K11863] [EC:3.4.22.-]
102266960  MAPK9; mitogen-activated protein kinase 9 isoform X1 [KO:K04440] [EC:2.7.11.24]
102267061  UGGT2; UDP-glucose:glycoprotein glucosyltransferase 2 isoform X2 [KO:K11718] [EC:2.4.1.-]
102267080  NSFL1C; NSFL1 cofactor p47 [KO:K14012]
102267259  XBP1; LOW QUALITY PROTEIN: X-box-binding protein 1 [KO:K09027]
102267415  SSR3; translocon-associated protein subunit gamma [KO:K13251]
102267423  ATF4; cyclic AMP-dependent transcription factor ATF-4 [KO:K04374]
102267585  STT3B; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B [KO:K07151] [EC:2.4.99.18]
102267812  DNAJC3; dnaJ homolog subfamily C member 3 [KO:K09523]
102267877  MARCHF6; E3 ubiquitin-protein ligase MARCHF6 [KO:K10661] [EC:2.3.2.27]
102268014  ERLEC1; endoplasmic reticulum lectin 1 [KO:K14008]
102268088  HSP90AA1; heat shock protein HSP 90-alpha [KO:K04079]
102268112  UBE2J1; ubiquitin-conjugating enzyme E2 J1 [KO:K10578] [EC:2.3.2.23]
102268121  UGGT1; UDP-glucose:glycoprotein glucosyltransferase 1 isoform X1 [KO:K11718] [EC:2.4.1.-]
102268367  SAR1A; small COPII coat GTPase SAR1A [KO:K07953] [EC:3.6.5.-]
102268592  BCL2; apoptosis regulator Bcl-2 isoform X1 [KO:K02161]
102268621  TRAM1; translocating chain-associated membrane protein 1 isoform X1 [KO:K14010]
102268820  HSP90B1; endoplasmin [KO:K09487]
102269051  SEC61G; protein transport protein Sec61 subunit gamma [KO:K07342]
102269068  DNAJB11; dnaJ homolog subfamily B member 11 [KO:K09517]
102269076  UBE4B; ubiquitin conjugation factor E4 B isoform X1 [KO:K10597] [EC:2.3.2.27]
102269190  DNAJA1; dnaJ homolog subfamily A member 1 isoform X1 [KO:K09502]
102269355  RAD23B; UV excision repair protein RAD23 homolog B [KO:K10839]
102269565  AMFR; E3 ubiquitin-protein ligase AMFR [KO:K10636] [EC:2.3.2.36]
102269574  MAN1A1; mannosyl-oligosaccharide 1,2-alpha-mannosidase IA [KO:K01230] [EC:3.2.1.113]
102269580  GANAB; neutral alpha-glucosidase AB [KO:K05546] [EC:3.2.1.207]
102269623  YOD1; ubiquitin thioesterase OTU1 isoform X1 [KO:K13719] [EC:3.1.2.-]
102269640  PREB; guanine nucleotide-exchange factor SEC12 isoform X1 [KO:K14003]
102270030  ERO1A; LOW QUALITY PROTEIN: ERO1-like protein alpha [KO:K10950] [EC:1.8.4.-]
102270045  LMAN2; vesicular integral-membrane protein VIP36 [KO:K10082]
102270105  EDEM1; ER degradation-enhancing alpha-mannosidase-like protein 1 isoform X1 [KO:K10084]
102270304  PRKN; E3 ubiquitin-protein ligase parkin isoform X1 [KO:K04556] [EC:2.3.2.31]
102270320  BAG1; BAG family molecular chaperone regulator 1 [KO:K09555]
102270482  KRTCAP2; LOW QUALITY PROTEIN: dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2 [KO:K28202]
102270542  DNAJC5; dnaJ homolog subfamily C member 5 [KO:K09525]
102270639  TXNDC5; thioredoxin domain-containing protein 5 [KO:K13984] [EC:5.3.4.1]
102270672  SYVN1; E3 ubiquitin-protein ligase synoviolin [KO:K10601] [EC:2.3.2.27]
102270759  EIF2AK3; eukaryotic translation initiation factor 2-alpha kinase 3 [KO:K08860] [EC:2.7.11.1]
102270765  EIF2S1; eukaryotic translation initiation factor 2 subunit 1 [KO:K03237]
102270771  DNAJC10; dnaJ homolog subfamily C member 10 [KO:K09530] [EC:1.8.4.-]
102270797  WFS1; wolframin [KO:K14020]
102270979  TRAM1L1; translocating chain-associated membrane protein 1-like 1 [KO:K14010]
102271287  UBXN1; UBX domain-containing protein 1 isoform X1 [KO:K24348]
102271636  VCP; transitional endoplasmic reticulum ATPase [KO:K13525]
102271661  MOGS; mannosyl-oligosaccharide glucosidase [KO:K01228] [EC:3.2.1.106]
102272175  SEL1L; protein sel-1 homolog 1 [KO:K14026]
102272181  SEC13; protein SEC13 homolog [KO:K14004]
102272225  UBQLN3; LOW QUALITY PROTEIN: ubiquilin-3 [KO:K04523]
102272421  MAPK10; mitogen-activated protein kinase 10 [KO:K04440] [EC:2.7.11.24]
102272520  BCAP31; B-cell receptor-associated protein 31 [KO:K14009]
102272638  MAP2K7; dual specificity mitogen-activated protein kinase kinase 7 isoform X1 [KO:K04431] [EC:2.7.12.2]
102272651  EDEM3; ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X2 [KO:K10086]
102272685  UFD1; ubiquitin recognition factor in ER-associated degradation protein 1 [KO:K14016]
102272719  RBX1; E3 ubiquitin-protein ligase RBX1 isoform X3 [KO:K03868] [EC:2.3.2.32]
102272788  DERL2; derlin-2 isoform X1 [KO:K13989]
102272979  UBE2D4; ubiquitin-conjugating enzyme E2 D4 isoform X1 [KO:K06689] [EC:2.3.2.23]
102273291  ERO1B; ERO1-like protein beta isoform X1 [KO:K10976] [EC:1.8.4.-]
102273703  PDIA4; protein disulfide-isomerase A4 [KO:K09582] [EC:5.3.4.1]
102273821  HSPA6; heat shock 70 kDa protein 6 [KO:K03283]
102273898  HSPA8; heat shock cognate 71 kDa protein [KO:K03283]
102273947  DDOST; dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit [KO:K12670]
102274566  DNAJA2; dnaJ homolog subfamily A member 2 [KO:K09503]
102274656  DNAJC5B; dnaJ homolog subfamily C member 5B [KO:K09525]
102274690  ATF6; cyclic AMP-dependent transcription factor ATF-6 alpha [KO:K09054]
102274847  NGLY1; LOW QUALITY PROTEIN: peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase [KO:K01456] [EC:3.5.1.52]
102274963  TMEM258; transmembrane protein 258 [KO:K26502]
102275172  ERN1; serine/threonine-protein kinase/endoribonuclease IRE1 isoform X1 [KO:K08852] [EC:2.7.11.1 3.1.26.-]
102275186  UBE2J2; ubiquitin-conjugating enzyme E2 J2 [KO:K04554] [EC:2.3.2.23]
102275265  TRAF2; TNF receptor-associated factor 2 [KO:K03173] [EC:2.3.2.27]
102275440  CALR; calreticulin [KO:K08057]
102275615  UBXN6; UBX domain-containing protein 6 isoform X2 [KO:K14011]
102275672  SEC23B; protein transport protein Sec23B [KO:K14006]
102275727  RAD23A; UV excision repair protein RAD23 homolog A isoform X1 [KO:K10839]
102276103  SEL1L2; protein sel-1 homolog 2 [KO:K14026]
102276298  CAPN2; calpain-2 catalytic subunit [KO:K03853] [EC:3.4.22.53]
102276425  SSR4; translocon-associated protein subunit delta isoform X2 [KO:K04571]
102276485  SIL1; nucleotide exchange factor SIL1 isoform X2 [KO:K14001]
102276819  DERL1; derlin-1 [KO:K11519]
102276849  MAP3K5; LOW QUALITY PROTEIN: mitogen-activated protein kinase kinase kinase 5 [KO:K04426] [EC:2.7.11.25]
102276957  UBE2G1; ubiquitin-conjugating enzyme E2 G1 isoform X1 [KO:K10575] [EC:2.3.2.23]
102277130  HSP90AB1; heat shock protein HSP 90-beta [KO:K04079]
102277183  TUSC3; tumor suppressor candidate 3 isoform X3 [KO:K19478]
102277240  [KO:K23741]
102277514  CUL1; cullin-1 [KO:K03347]
102277662  ATXN3; ataxin-3 isoform X1 [KO:K11863] [EC:3.4.22.-]
102277805  SEC31A; protein transport protein Sec31A isoform X1 [KO:K14005]
102277814  MAN1B1; endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase isoform X1 [KO:K23741]
102277976  MAPK8; mitogen-activated protein kinase 8 isoform X1 [KO:K04440] [EC:2.7.11.24]
102278011  MAGT1; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit MAGT1 [KO:K19478]
102278147  CANX; calnexin [KO:K08054]
102278697  [KO:K03283]
102278721  SSR2; translocon-associated protein subunit beta isoform X1 [KO:K13250]
102278791  STT3A; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A [KO:K07151] [EC:2.4.99.18]
102278817  SEC24C; protein transport protein Sec24C isoform X1 [KO:K14007]
102278888  UBXN2A; UBX domain-containing protein 2A [KO:K24349]
102278977  [KO:K03283]
102279168  UBQLN2; ubiquilin-2 [KO:K04523]
102279181  UBQLN4; ubiquilin-4 [KO:K04523]
102279285  UBXN4; UBX domain-containing protein 4 isoform X1 [KO:K24348]
102279292  OS9; protein OS-9 isoform X1 [KO:K10088]
102279382  DERL3; derlin-3 isoform X1 [KO:K13989]
102279693  DNAJB1; dnaJ homolog subfamily B member 1 [KO:K09507]
102279740  BAX; apoptosis regulator BAX isoform X1 [KO:K02159]
102280148  UBQLN1; ubiquilin-1 isoform X1 [KO:K04523]
102280586  MBTPS2; membrane-bound transcription factor site-2 protease isoform X3 [KO:K07765] [EC:3.4.24.85]
102281072  SELENOS; selenoprotein S isoform X1 [KO:K14025]
102281073  UBE2D2; ubiquitin-conjugating enzyme E2 D2 isoform X2 [KO:K06689] [EC:2.3.2.23]
102281496  DNAJB2; dnaJ homolog subfamily B member 2 isoform X1 [KO:K09508]
102281691  PDIA3; protein disulfide-isomerase A3 [KO:K08056] [EC:5.3.4.1]
102281711  [KO:K12666]
102282274  SEC61B; protein transport protein Sec61 subunit beta [KO:K09481]
102282290  FBXO2; F-box only protein 2 isoform X1 [KO:K10099]
102282354  [KO:K08057]
102282369  HERPUD1; homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein isoform X1 [KO:K14027]
102282581  RRBP1; ribosome-binding protein 1 isoform X1 [KO:K14000]
102282642  SEC63; translocation protein SEC63 homolog [KO:K09540]
102282645  BAG2; BAG family molecular chaperone regulator 2 isoform X1 [KO:K09556]
102282666  LMAN1L; protein ERGIC-53-like [KO:K10081]
102282772  P4HB; protein disulfide-isomerase [KO:K09580] [EC:5.3.4.1]
102283099  CAPN1; calpain-1 catalytic subunit [KO:K01367] [EC:3.4.22.52]
102283265  RNF185; E3 ubiquitin-protein ligase RNF185 [KO:K10666] [EC:2.3.2.27]
102283374  HSPA5; endoplasmic reticulum chaperone BiP [KO:K09490] [EC:3.6.4.10]
102283493  UBE2G2; ubiquitin-conjugating enzyme E2 G2 isoform X2 [KO:K04555] [EC:2.3.2.23]
102283500  NFE2L2; nuclear factor erythroid 2-related factor 2 isoform X2 [KO:K05638]
102283876  SEC61A2; protein transport protein Sec61 subunit alpha isoform X1 [KO:K10956]
102284064  CRYAB; alpha-crystallin B chain [KO:K09542]
102284075  PLAA; phospholipase A-2-activating protein isoform X1 [KO:K14018]
102284783  DAD1; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 [KO:K12668]
102284851  SEC62; translocation protein SEC62 [KO:K12275]
102285027  DNAJB12; dnaJ homolog subfamily B member 12 isoform X1 [KO:K09518]
102285636  UBE2D3; ubiquitin-conjugating enzyme E2 D3 isoform X4 [KO:K06689] [EC:2.3.2.23]
102285821  RPN2; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 isoform X2 [KO:K12667]
102285878  FBXO6; F-box only protein 6 isoform X1 [KO:K10100]
102285944  HSPA1L; heat shock 70 kDa protein 1-like isoform X2 [KO:K03283]
102286126  MBTPS1; membrane-bound transcription factor site-1 protease isoform X1 [KO:K08653] [EC:3.4.21.112]
102286188  UBE2D1; ubiquitin-conjugating enzyme E2 D1 isoform X1 [KO:K06689] [EC:2.3.2.23]
102286189  MAN1C1; mannosyl-oligosaccharide 1,2-alpha-mannosidase IC isoform X1 [KO:K01230] [EC:3.2.1.113]
102286235  SEC31B; protein transport protein Sec31B isoform X1 [KO:K14005]
102286306  SEC23A; LOW QUALITY PROTEIN: protein transport protein Sec23A [KO:K14006]
102286617  CRYAA; alpha-crystallin A chain [KO:K09541]
102287255  EDEM2; ER degradation-enhancing alpha-mannosidase-like protein 2 [KO:K10085]
102287418  SSR1; translocon-associated protein subunit alpha isoform X1 [KO:K13249]
102287419  CKAP4; cytoskeleton-associated protein 4 [KO:K13999]
102287436  SEC24D; protein transport protein Sec24D isoform X1 [KO:K14007]
102287645  HSPA4L; heat shock 70 kDa protein 4L [KO:K09485]
102288160  SEC24A; protein transport protein Sec24A isoform X1 [KO:K14007]
102288163  PRKCSH; glucosidase 2 subunit beta [KO:K08288]
102288212  ATF6B; cyclic AMP-dependent transcription factor ATF-6 beta isoform X4 [KO:K09049]
106700646  SVIP; small VCP/p97-interacting protein [KO:K14014]
138983909  DDIT3; DNA damage-inducible transcript 3 protein [KO:K04452]
138988497  [KO:K07953] [EC:3.6.5.-]
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
bom00510  N-Glycan biosynthesis
bom03050  Proteasome
bom03060  Protein export
bom04210  Apoptosis
bom04930  Type II diabetes mellitus
bom05010  Alzheimer disease
bom05012  Parkinson disease
bom05020  Prion disease
KO pathway
ko04141   

DBGET integrated database retrieval system