KEGG   PATHWAY: atr04141
Entry
atr04141                    Pathway                                
Name
Protein processing in endoplasmic reticulum - Amborella trichopoda
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
atr04141  Protein processing in endoplasmic reticulum
atr04141

Other DBs
GO: 0030433 0034976
Organism
Amborella trichopoda [GN:atr]
Gene
18442675  protein transport protein Sec61 subunit alpha [KO:K10956]
18435421  preprotein translocase subunit SCY1, chloroplastic [KO:K10956]
18440435  protein transport protein Sec61 subunit beta [KO:K09481]
18442024  protein transport protein Sec61 subunit beta [KO:K09481]
105420854  protein transport protein Sec61 subunit gamma-1 [KO:K07342]
18438019  protein transport protein Sec61 subunit gamma-1 [KO:K07342]
18428968  uncharacterized protein LOC18428968 [KO:K12275]
18421948  dnaJ protein ERDJ2A [KO:K09540]
18995797  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1B [KO:K12666]
18445453  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1A [KO:K12666]
18447158  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 [KO:K12667]
18440537  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 isoform X1 [KO:K12668]
18445912  dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit [KO:K12670]
18443362  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A [KO:K07151] [EC:2.4.99.18]
18437593  dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B [KO:K07151] [EC:2.4.99.18]
18425473  probable dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3B [KO:K19478]
18435666  oligosaccharyltransferase complex subunit ostc [KO:K26501]
18448193  transmembrane protein 258 [KO:K26502]
18438178  mannosyl-oligosaccharide glucosidase GCS1 isoform X1 [KO:K01228] [EC:3.2.1.106]
18435884  heat shock 70 kDa protein 17 [KO:K09486]
18423094  luminal-binding protein [KO:K09490] [EC:3.6.4.10]
18429053  luminal-binding protein [KO:K09490] [EC:3.6.4.10]
18445100  dnaJ protein ERDJ3B [KO:K09517]
18427397  dnaJ protein P58IPK homolog B isoform X1 [KO:K09523]
18433953  heat shock protein 90-5, chloroplastic [KO:K09487]
18441623  endoplasmin homolog [KO:K09487]
18438811  heat shock protein 90-6, mitochondrial [KO:K09487]
18447023  probable glucan 1,3-alpha-glucosidase [KO:K05546] [EC:3.2.1.207]
105421894  glucosidase 2 subunit beta isoform X1 [KO:K08288]
18434560  calnexin homolog [KO:K08054]
18431222  calreticulin [KO:K08057]
18437267  calreticulin [KO:K08057]
18448729  calreticulin-3 [KO:K08057]
18435677  mannosyl-oligosaccharide 1,2-alpha-mannosidase MNS1 isoform X2 [KO:K01230] [EC:3.2.1.113]
18435237  mannosyl-oligosaccharide 1,2-alpha-mannosidase MNS3 [KO:K23741] [EC:3.2.1.209]
18429367  SEC12-like protein 1 [KO:K14003]
18436373  SEC12-like protein 2 [KO:K14003]
18431236  GTP-binding protein SAR1A [KO:K07953] [EC:3.6.5.-]
18431231  GTP-binding protein SAR1A [KO:K07953] [EC:3.6.5.-]
18427102  protein transport protein SEC13 homolog B [KO:K14004]
18444311  protein transport protein SEC13 homolog B [KO:K14004]
18428304  protein transport protein SEC31 homolog B isoform X1 [KO:K14005]
18423254  protein transport protein SEC23 [KO:K14006]
18429512  protein transport protein SEC23 [KO:K14006]
18443891  protein transport protein SEC23 [KO:K14006]
18448291  protein transport protein Sec24-like At3g07100 [KO:K14007]
18447425  protein transport protein Sec24-like At4g32640 [KO:K14007]
18448413  UDP-glucose:glycoprotein glucosyltransferase [KO:K11718] [EC:2.4.1.-]
18427634  alpha-mannosidase I MNS5 isoform X1 [KO:K10084]
18429526  alpha-mannosidase I MNS4 isoform X1 [KO:K10085]
18426585  protein disulfide isomerase-like 1-6 [KO:K09580] [EC:5.3.4.1]
18432901  protein disulfide-isomerase [KO:K09580] [EC:5.3.4.1]
18448111  protein disulfide-isomerase 5-2 [KO:K09580] [EC:5.3.4.1]
18444278  protein disulfide isomerase-like 1-4 [KO:K09580] [EC:5.3.4.1]
18424869  protein disulfide isomerase-like 2-3 [KO:K09584] [EC:5.3.4.1]
18445105  protein disulfide-isomerase like 2-1 [KO:K09584] [EC:5.3.4.1]
18429322  endoplasmic reticulum oxidoreductin-1 [KO:K10950] [EC:1.8.4.-]
18442547  protein OS-9 homolog isoform X1 [KO:K10088]
18441696  translocon-associated protein subunit alpha [KO:K13249]
18434410  translocon-associated protein subunit beta isoform X1 [KO:K13250]
18425930  B-cell receptor-associated protein 31 [KO:K14009]
18436968  B-cell receptor-associated protein 31 isoform X1 [KO:K14009]
18443467  derlin-1 isoform X2 [KO:K13989]
18447987  derlin-2 isoform X1 [KO:K13989]
18440118  protein PRRC2C isoform X1 [KO:K24348]
18448514  plant UBX domain-containing protein 11 isoform X1 [KO:K24348]
18423871  plant UBX domain-containing protein 2 [KO:K14011]
18428169  plant UBX domain-containing protein 4 isoform X2 [KO:K14012]
18426439  cell division control protein 48 homolog D [KO:K13525]
18430769  cell division cycle protein 48 homolog [KO:K13525]
18445166  NPL4-like protein 1 [KO:K14015]
18446926  ubiquitin fusion degradation protein 1 homolog isoform X1 [KO:K14016]
18436169  ubiquitin fusion degradation protein 1 homolog isoform X1 [KO:K14016]
18431198  ubiquitin fusion degradation protein 1 homolog [KO:K14016]
18442078  ubiquitin fusion degradation protein 1 homolog [KO:K14016]
105421653  LOW QUALITY PROTEIN: ubiquitin fusion degradation protein 1 homolog [KO:K14016]
18448346  stromal 70 kDa heat shock-related protein, chloroplastic [KO:K03283]
18421799  heat shock 70 kDa protein 5 [KO:K03283]
18426511  heat shock cognate 70 kDa protein 2 [KO:K03283]
18428205  dnaJ protein homolog 2 [KO:K09503]
18421632  dnaJ protein homolog [KO:K09503]
18430356  chaperone protein dnaJ 49 [KO:K09518]
18428425  chaperone protein dnaJ 49 [KO:K09518]
18424137  heat shock protein 83 [KO:K04079]
18447377  heat shock protein 81-1 isoform X2 [KO:K04079]
18436205  uncharacterized protein LOC18436205 [KO:K09562]
18434645  hsp70 nucleotide exchange factor FES1 [KO:K09562]
18421862  17.3 kDa class I heat shock protein [KO:K13993]
18422336  15.7 kDa heat shock protein, peroxisomal [KO:K13993]
18422995  17.8 kDa class I heat shock protein [KO:K13993]
18422377  18.1 kDa class I heat shock protein [KO:K13993]
18431890  26.5 kDa heat shock protein, mitochondrial isoform X2 [KO:K13993]
18423683  17.8 kDa class I heat shock protein [KO:K13993]
18432984  17.1 kDa class II heat shock protein [KO:K13993]
18432985  17.1 kDa class II heat shock protein [KO:K13993]
18432990  17.1 kDa class II heat shock protein [KO:K13993]
18432991  17.3 kDa class II heat shock protein [KO:K13993]
18432992  17.1 kDa class II heat shock protein [KO:K13993]
18426534  small heat shock protein, chloroplastic [KO:K13993]
18441877  small heat shock protein, chloroplastic [KO:K13993]
18440189  17.8 kDa class I heat shock protein [KO:K13993]
18440190  17.5 kDa class I heat shock protein [KO:K13993]
18440220  16.9 kDa class I heat shock protein 2 [KO:K13993]
18440221  17.8 kDa class I heat shock protein [KO:K13993]
18443792  17.8 kDa class I heat shock protein [KO:K13993]
18443793  17.8 kDa class I heat shock protein [KO:K13993]
105420281  18.8 kDa class II heat shock protein-like [KO:K13993]
105421107  class I heat shock protein-like [KO:K13993]
18427818  LOW QUALITY PROTEIN: 22.7 kDa class IV heat shock protein-like [KO:K13993]
18448031  15.4 kDa class V heat shock protein [KO:K13993]
18445646  ubiquitin thioesterase OTU1 [KO:K13719] [EC:3.1.2.-]
18445937  phospholipase A-2-activating protein isoform X2 [KO:K14018]
18435340  ubiquitin receptor RAD23b [KO:K10839]
18995758  ubiquitin receptor RAD23d [KO:K10839]
18424054  ubiquitin domain-containing protein DSK2b isoform X1 [KO:K04523]
18443204  peptide-N(4)-(N-acetyl-beta- glucosaminyl)asparagine amidase [KO:K01456] [EC:3.5.1.52]
18438476  probable ubiquitin conjugation factor E4 [KO:K10597] [EC:2.3.2.27]
18426694  eukaryotic translation initiation factor 2 subunit alpha homolog isoform X1 [KO:K03237]
18426576  subtilisin-like protease SBT6.1 [KO:K08653] [EC:3.4.21.112]
18448966  membrane-bound transcription factor site-2 protease homolog isoform X2 [KO:K07765] [EC:3.4.24.85]
18445485  serine/threonine-protein kinase/endoribonuclease IRE1a isoform X1 [KO:K08852] [EC:2.7.11.1 3.1.26.-]
18424404  serine/threonine-protein kinase/endoribonuclease IRE1a isoform X1 [KO:K08852] [EC:2.7.11.1 3.1.26.-]
18424407  serine/threonine-protein kinase/endoribonuclease IRE1a [KO:K08852] [EC:2.7.11.1 3.1.26.-]
18440303  probable E3 ubiquitin ligase SUD1 isoform X1 [KO:K10661] [EC:2.3.2.27]
18430216  ubiquitin-conjugating enzyme E2 32 [KO:K10578] [EC:2.3.2.23]
18423951  ubiquitin-conjugating enzyme E2 34 [KO:K04554] [EC:2.3.2.23]
18436042  ubiquitin-conjugating enzyme E2 7 [KO:K10575] [EC:2.3.2.23]
18431516  ubiquitin-conjugating enzyme E2 7 isoform X1 [KO:K10575] [EC:2.3.2.23]
18448598  ERAD-associated E3 ubiquitin-protein ligase HRD1B [KO:K10601] [EC:2.3.2.27]
18439309  uncharacterized protein LOC18439309 [KO:K10666] [EC:2.3.2.27]
18443888  uncharacterized protein LOC18443888 [KO:K10666] [EC:2.3.2.27]
18423131  E3 ubiquitin-protein ligase RMA2 [KO:K10666] [EC:2.3.2.27]
18445939  E3 ubiquitin-protein ligase RNF185 isoform X2 [KO:K10666] [EC:2.3.2.27]
18423761  ERAD-associated E3 ubiquitin-protein ligase component HRD3A [KO:K14026]
18436990  E3 ubiquitin protein ligase RIN2 isoform X1 [KO:K10636] [EC:2.3.2.36]
18427839  E3 ubiquitin-protein ligase CHIP [KO:K09561] [EC:2.3.2.27]
18429949  ubiquitin-conjugating enzyme E2 11 [KO:K06689] [EC:2.3.2.23]
18447406  ubiquitin-conjugating enzyme E2-17 kDa [KO:K06689] [EC:2.3.2.23]
18432387  ubiquitin-conjugating enzyme E2 10 [KO:K06689] [EC:2.3.2.23]
18439128  ubiquitin-conjugating enzyme E2-17 kDa isoform X2 [KO:K06689] [EC:2.3.2.23]
18429920  ubiquitin-conjugating enzyme E2-17 kDa [KO:K06689] [EC:2.3.2.23]
18436642  ubiquitin-conjugating enzyme E2-17 kDa isoform X2 [KO:K06689] [EC:2.3.2.23]
18439492  RING-box protein 1a [KO:K03868] [EC:2.3.2.32]
105421056  RING-box protein 1a-like isoform X1 [KO:K03868] [EC:2.3.2.32]
18422906  cullin-1 [KO:K03347]
105420412  SKP1-like protein 1B [KO:K03094]
105420640  SKP1-like protein 12 [KO:K03094]
105420531  SKP1-like protein 12 [KO:K03094]
105421410  SKP1-like protein 11 [KO:K03094]
105421411  SKP1-like protein 11 [KO:K03094]
18437706  SKP1-like protein 1A [KO:K03094]
105421420  SKP1-like protein 4 [KO:K03094]
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
atr00510  N-Glycan biosynthesis
atr03050  Proteasome
atr03060  Protein export
KO pathway
ko04141   
LinkDB

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