KEGG   PATHWAY: dre04120
Entry
dre04120                    Pathway                                
Name
Ubiquitin mediated proteolysis - Danio rerio (zebrafish)
Description
Protein ubiquitination plays an important role in eukaryotic cellular processes. It mainly functions as a signal for 26S proteasome dependent protein degradation. The addition of ubiquitin to proteins being degraded is performed by a reaction cascade consisting of three enzymes, named E1 (ubiquitin activating enzyme), E2 (ubiquitin conjugating enzyme), and E3 (ubiquitin ligase). Each E3 has specificity to its substrate, or proteins to be targeted by ubiquitination. Many E3s are discovered in eukaryotes and they are classified into four types: HECT type, U-box type, single RING-finger type, and multi-subunit RING-finger type. Multi-subunit RING-finger E3s are exemplified by cullin-Rbx E3s and APC/C. They consist of a RING-finger-containing subunit (RBX1 or RBX2) that functions to bind E2s, a scaffold-like cullin molecule, adaptor proteins, and a target recognizing subunit that binds substrates.
Class
Genetic Information Processing; Folding, sorting and degradation
Pathway map
dre04120  Ubiquitin mediated proteolysis
dre04120

Other DBs
GO: 0016567
Organism
Danio rerio (zebrafish) [GN:dre]
Gene
100000479  ube2g1b; ubiquitin-conjugating enzyme E2G 1b [KO:K10575] [EC:2.3.2.23]
100001302  uba7; ubiquitin-like modifier-activating enzyme 1 [KO:K03178] [EC:6.2.1.45]
100001914  ube2d4; ubiquitin-conjugating enzyme E2 D4 [KO:K06689] [EC:2.3.2.23]
100003587  herc3; probable E3 ubiquitin-protein ligase HERC3 [KO:K10614] [EC:2.3.2.26]
100003679  keap1b; kelch-like ECH-associated protein 1B isoform X1 [KO:K10456]
100004133  ddb2; DNA damage-binding protein 2 [KO:K10140]
100006147  cul5b; cullin-5 isoform X3 [KO:K10612]
100007521  socs1b; suppressor of cytokine signaling 1b [KO:K04694]
100007662  airE; autoimmune regulator [KO:K10603]
100037384  ube2j2; ubiquitin-conjugating enzyme E2 J2 [KO:K04554] [EC:2.3.2.23]
100037391  cop1; E3 ubiquitin-protein ligase COP1 [KO:K10143] [EC:2.3.2.27]
100073331  birc7; baculoviral IAP repeat-containing protein 7 isoform 2 [KO:K16061]
100136859  fbxw8; F-box/WD repeat-containing protein 8 [KO:K10264]
100148091  herc56.4; E3 ISG15--protein ligase HERC5.4 [KO:K10615] [EC:2.3.2.26]
100148604  fzr1b; fizzy-related protein homolog isoform X1 [KO:K03364]
100151173  si:rp71-68n21.9; kelch-like protein 9 isoform X2 [KO:K10447]
100318335  anapc2; anaphase-promoting complex subunit 2 [KO:K03349]
100319387  fbxo4; F-box only protein 4 isoform X1 [KO:K10291]
100330031  itchb; itchy E3 ubiquitin protein ligase B [KO:K05632] [EC:2.3.2.26]
100330952  mid1; E3 ubiquitin-protein ligase Midline-1 isoform X1 [KO:K08285] [EC:2.3.2.27]
100331274  itcha; itchy E3 ubiquitin protein ligase A [KO:K05632] [EC:2.3.2.26]
100331775  [KO:K10581] [EC:2.3.2.24]
100334486  map3k1; mitogen-activated protein kinase kinase kinase 1 isoform X1 [KO:K04416] [EC:2.7.11.25]
100537290  rhobtb1; rho-related BTB domain-containing protein 1 isoform X1 [KO:K07868]
103909792  wwp1; NEDD4-like E3 ubiquitin-protein ligase WWP1 isoform X1 [KO:K05633] [EC:2.3.2.26]
114445  ube2ia; SUMO-conjugating enzyme UBC9-B [KO:K10577]
170784  ube4b; ubiquitin conjugation factor E4 B [KO:K10597] [EC:2.3.2.27]
192341  eloB; elongin-B [KO:K03873]
30100  ube2kb; ubiquitin-conjugating enzyme E2Kb (UBC1 homolog, yeast) [KO:K04649] [EC:2.3.2.23]
30450  cdc27; cell division cycle protein 27 homolog [KO:K03350]
30622  ube2ib; SUMO-conjugating enzyme UBC9-A [KO:K10577]
30637  mdm2; E3 ubiquitin-protein ligase Mdm2 isoform 1 [KO:K06643] [EC:2.3.2.27]
321544  prpf19; pre-mRNA-processing factor 19 [KO:K10599] [EC:2.3.2.27]
321689  ube2e3; ubiquitin-conjugating enzyme E2 E3 [KO:K20217] [EC:2.3.2.23]
321695  smurf1; E3 ubiquitin-protein ligase SMURF1 [KO:K04678] [EC:2.3.2.26]
321832  ube2d3; ubiquitin-conjugating enzyme E2 D3 [KO:K06689] [EC:2.3.2.23]
321837  keap1a; kelch-like ECH-associated protein 1A [KO:K10456]
321875  rchy1; RING finger and CHY zinc finger domain-containing protein 1 [KO:K10144] [EC:2.3.2.27]
321943  ube2l3b; ubiquitin-conjugating enzyme E2 L3b [KO:K04552] [EC:2.3.2.23]
322854  anapc5; anaphase-promoting complex subunit 5 [KO:K03352]
323883  cul1a; cullin-1a isoform X1 [KO:K03347]
323951  klhl13; kelch-like protein 13 isoform 2 [KO:K10447]
324015  ube2d1b; ubiquitin-conjugating enzyme E2 D1b [KO:K06689] [EC:2.3.2.23]
324089  det1; DET1 homolog isoform X1 [KO:K10571]
324237  trim37; E3 ubiquitin-protein ligase TRIM37 [KO:K10608] [EC:2.3.2.27]
324243  stub1; E3 ubiquitin-protein ligase CHIP isoform X1 [KO:K09561] [EC:2.3.2.27]
324655  cul3a; cullin-3a [KO:K03869]
325470  ube2al; ubiquitin conjugating enzyme E2 A, like [KO:K10573] [EC:2.3.2.23]
327215  cul5a; cullin-5a [KO:K10612]
334133  ube2g1a; ubiquitin-conjugating enzyme E2 G1a [KO:K10575] [EC:2.3.2.23]
334373  fbxw11a; F-box and WD repeat domain-containing 11-A [KO:K03362]
334627  ubr5; E3 ubiquitin-protein ligase UBR5 [KO:K10593] [EC:2.3.2.26]
335226  syvn1; E3 ubiquitin-protein ligase synoviolin [KO:K10601] [EC:2.3.2.27]
335409  socs3a; suppressor of cytokine signaling 3a [KO:K04696]
335444  ube2d2l; ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast), like [KO:K06689] [EC:2.3.2.23]
336088  cul2; cullin-2 [KO:K03870]
336542  [KO:K08770]
336598  herc1; probable E3 ubiquitin-protein ligase HERC1 isoform X1 [KO:K10594] [EC:2.3.2.26]
337810  rps27a; ubiquitin-ribosomal protein eS31 fusion protein [KO:K02977]
368425  ube2h; ubiquitin-conjugating enzyme E2 H [KO:K10576] [EC:2.3.2.23]
373107  birc2; baculoviral IAP repeat-containing protein 2 [KO:K16060]
373108  xiaP; E3 ubiquitin-protein ligase XIAP [KO:K04725] [EC:2.3.2.27]
393223  fzr1a; fizzy/cell division cycle 20 related 1a [KO:K03364]
393313  ube2nb; ubiquitin-conjugating enzyme E2Nb [KO:K10580] [EC:2.3.2.23]
393314  pias4b; E3 SUMO-protein ligase PIAS4b isoform 2 [KO:K16065] [EC:2.3.2.27]
393445  ube3c; ubiquitin-protein ligase E3C [KO:K10589] [EC:2.3.2.26]
393599  ddb1; DNA damage-binding protein 1 [KO:K10610]
393716  skp1; S-phase kinase-associated protein 1 [KO:K03094]
393907  cdc23; cell division cycle protein 23 homolog [KO:K03355]
393933  cdc34a; Cell division cycle 34 homolog (S. cerevisiae) A [KO:K02207] [EC:2.3.2.23]
393934  ube2d2; ubiquitin-conjugating enzyme E2 D2 [KO:K06689] [EC:2.3.2.23]
393966  ppil2; RING-type E3 ubiquitin-protein ligase PPIL2 [KO:K10598] [EC:5.2.1.8]
394002  cul4a; cullin-4A [KO:K10609]
394085  ube2d1a; ubiquitin-conjugating enzyme E2 D1a [KO:K06689] [EC:2.3.2.23]
402829  ubox5; RING finger protein 37 [KO:K10600] [EC:2.3.2.27]
406255  fancl; E3 ubiquitin-protein ligase FANCL [KO:K10606] [EC:2.3.2.27]
406260  ube2q2; ubiquitin-conjugating enzyme E2 Q2 isoform 1 [KO:K10582] [EC:2.3.2.23]
406335  uba1; ubiquitin-like modifier-activating enzyme 1 [KO:K03178] [EC:6.2.1.45]
406353  cdc20; cell division cycle protein 20 homolog [KO:K03363]
406596  socs3b; suppressor of cytokine signaling 3b [KO:K04696]
406606  ube2f; NEDD8-conjugating enzyme UBE2F [KO:K10687] [EC:2.3.2.34]
406672  uba2; SUMO-activating enzyme subunit 2 [KO:K10685] [EC:6.2.1.45]
406712  pias4a; E3 SUMO-protein ligase PIAS4-A [KO:K16065] [EC:2.3.2.27]
406776  uba3; NEDD8-activating enzyme E1 catalytic subunit [KO:K10686] [EC:6.2.1.64]
406794  ube2j1; ubiquitin-conjugating enzyme E2 J1 [KO:K10578] [EC:2.3.2.23]
406807  ube2na; ubiquitin-conjugating enzyme E2Na [KO:K10580] [EC:2.3.2.23]
406816  cul1b; cullin-1b [KO:K03347]
406825  fbxw11b; F-box and WD repeat domain-containing 11-B [KO:K03362]
415148  sae1; SUMO-activating enzyme subunit 1 [KO:K10684] [EC:6.2.1.45]
415162  ube2l3a; ubiquitin-conjugating enzyme E2 L3a [KO:K04552] [EC:2.3.2.23]
436602  ube2z; ubiquitin-conjugating enzyme E2 Z [KO:K10585] [EC:2.3.2.23]
436713  elocb; elongin C paralog B [KO:K03872]
436873  ube2r2; ubiquitin-conjugating enzyme E2 R2 isoform X1 [KO:K02207] [EC:2.3.2.23]
436961  cdc34b; Cell division cycle 34 homolog (S. cerevisiae) B [KO:K02207] [EC:2.3.2.23]
437020  ube2b; ubiquitin-conjugating enzyme E2 B isoform X1 [KO:K10574] [EC:2.3.2.23]
445073  socs1a; suppressor of cytokine signaling 1a isoform X1 [KO:K04694]
445100  ube2e2; ubiquitin-conjugating enzyme E2 E2 [KO:K20217] [EC:2.3.2.23]
445501  cdc26; anaphase-promoting complex subunit CDC26 isoform X1 [KO:K03359]
447935  eloca; elongin C paralog A [KO:K03872]
449811  ercc8; DNA excision repair protein ERCC-8 [KO:K10570]
449846  rbx1; E3 ubiquitin-protein ligase RBX1 [KO:K03868] [EC:2.3.2.32]
492364  cbl; E3 ubiquitin-protein ligase CBL [KO:K04707] [EC:2.3.2.27]
494046  anapc4; anaphase-promoting complex subunit 4 isoform X1 [KO:K03351]
503534  rnf7; RING-box protein 2 [KO:K10611]
541355  ube2ka; ubiquitin-conjugating enzyme E2Ka (UBC1 homolog, yeast) [KO:K04649] [EC:2.3.2.23]
550134  ubb; polyubiquitin-B [KO:K08770]
550328  prkN; E3 ubiquitin-protein ligase parkin [KO:K04556] [EC:2.3.2.31]
550464  ube2g2; ubiquitin-conjugating enzyme E2 G2 [KO:K04555] [EC:2.3.2.23]
550576  anapc16; anaphase-promoting complex subunit 16 [KO:K25229]
553013  ube2wa; probable ubiquitin-conjugating enzyme E2 W-A [KO:K10688] [EC:2.3.2.23 2.3.2.25]
553327  mgrn1b; E3 ubiquitin-protein ligase MGRN1b [KO:K10604] [EC:2.3.2.27]
553415  rhobtb4; Rho related BTB domain containing 4 isoform 2 [KO:K07868]
553603  ube2q1; ubiquitin-conjugating enzyme E2 Q1 [KO:K10582] [EC:2.3.2.23]
554561  traf6; TNF receptor-associated factor 6 [KO:K03175] [EC:2.3.2.27]
556277  cblB; E3 ubiquitin-protein ligase CBL-B [KO:K22517] [EC:2.3.2.27]
556864  ube3b; ubiquitin-protein ligase E3B [KO:K10588] [EC:2.3.2.26]
557121  ube4a; ubiquitin conjugation factor E4 A isoform X2 [KO:K10596] [EC:2.3.2.27]
557472  ube2ql1; ubiquitin-conjugating enzyme E2Q-like protein 1 [KO:K10582] [EC:2.3.2.23]
557513  herc4; probable E3 ubiquitin-protein ligase HERC4 [KO:K10615] [EC:2.3.2.26]
558402  anapc7; anaphase-promoting complex subunit 7 [KO:K03354]
558479  herc2; E3 ubiquitin-protein ligase HERC2 isoform X2 [KO:K10595] [EC:2.3.2.26]
559439  huwe1; E3 ubiquitin-protein ligase HUWE1 isoform 1 [KO:K10592] [EC:2.3.2.26]
559634  nedd4l; E3 ubiquitin-protein ligase NEDD4-like isoform X33 [KO:K13305] [EC:2.3.2.26]
559776  fbxo2; F-box only protein 2 [KO:K10099]
559981  herc56.1; probable E3 ubiquitin-protein ligase HERC4 [KO:K10615] [EC:2.3.2.26]
560313  cul4b; cullin-4B [KO:K10609]
562014  cdc16; cell division cycle protein 16 homolog [KO:K03353]
562764  trim32; E3 ubiquitin-protein ligase TRIM32 [KO:K10607] [EC:2.3.2.27]
562982  pias1b; E3 SUMO-protein ligase PIAS1 isoform X1 [KO:K04706] [EC:2.3.2.-]
563542  ube2e1; ubiquitin-conjugating enzyme E2 E1 [KO:K20217] [EC:2.3.2.23]
563633  smurf2; E3 ubiquitin-protein ligase SMURF2 [KO:K04678] [EC:2.3.2.26]
563708  skp2; S-phase kinase-associated protein 2 [KO:K03875]
564149  pias2; E3 SUMO-protein ligase PIAS2 [KO:K16063] [EC:2.3.2.-]
564377  [KO:K10579] [EC:2.3.2.34]
564496  pias1a; E3 SUMO-protein ligase PIAS1 isoform X2 [KO:K04706] [EC:2.3.2.-]
564527  wwp2; NEDD4-like E3 ubiquitin-protein ligase WWP2 [KO:K05630] [EC:2.3.2.26]
564866  trip12; E3 ubiquitin-protein ligase TRIP12 [KO:K10590] [EC:2.3.2.26]
564991  fbxw7; F-box/WD repeat-containing protein 7 isoform X1 [KO:K10260]
565383  cblC; E3 ubiquitin-protein ligase CBL-C [KO:K22518] [EC:2.3.2.27]
565498  ube2s; ubiquitin-conjugating enzyme E2 S [KO:K10583] [EC:2.3.2.23]
565844  rhobtb2b; rho-related BTB domain-containing protein 2 isoform X1 [KO:K07868]
566441  ube2c; ubiquitin-conjugating enzyme E2 C [KO:K06688] [EC:2.3.2.23]
567370  uba6; ubiquitin-like modifier-activating enzyme 6 [KO:K10699] [EC:6.2.1.45]
567670  [KO:K10594] [EC:2.3.2.26]
568795  anapc1; anaphase-promoting complex subunit 1 isoform X2 [KO:K03348]
569473  anapc13; anaphase-promoting complex subunit 13 [KO:K12456]
572370  cul3b; cullin-3b [KO:K03869]
619412  nedd4a; E3 ubiquitin-protein ligase NEDD4 isoform X1 [KO:K10591] [EC:2.3.2.26]
641289  uba52; ubiquitin-ribosomal protein eL40 fusion protein [KO:K02927]
692325  ube2wb; probable ubiquitin-conjugating enzyme E2 W-B [KO:K10688] [EC:2.3.2.23 2.3.2.25]
751740  anapc15; anaphase-promoting complex subunit 15 [KO:K25228]
768140  anapc11; anaphase-promoting complex subunit 11 [KO:K03358]
777766  ubc; polyubiquitin-C [KO:K08770]
791202  vhl; von Hippel-Lindau disease tumor suppressor [KO:K03871]
792398  ube3a; ubiquitin-protein ligase E3A [KO:K10587] [EC:2.3.2.26]
792631  rhobtb2a; rho-related BTB domain-containing protein 2 isoform X1 [KO:K07868]
793939  mgrn1a; probable E3 ubiquitin-protein ligase MGRN1 isoform 2 [KO:K10604] [EC:2.3.2.27]
795635  vhlL; von Hippel-Lindau-like protein [KO:K03871]
796547  birc6; dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6 isoform X1 [KO:K10586] [EC:2.3.2.23]
797853  ube2a; ubiquitin-conjugating enzyme E2 A [KO:K10573] [EC:2.3.2.23]
798352  anapc10; anaphase-promoting complex subunit 10 isoform X1 [KO:K03357]
80955  siah1; E3 ubiquitin-protein ligase Siah1 [KO:K04506] [EC:2.3.2.27]
Reference
PMID:16922370
  Authors
Kamura T.
  Title
[Cullin-based E3 family]
  Journal
Tanpakushitsu Kakusan Koso 51:1167-72 (2006)
Reference
PMID:16922408
  Authors
Matsuda N.
  Title
[Overview: hereditary disorders caused by dysfunction of ubiquitylation]
  Journal
Tanpakushitsu Kakusan Koso 51:1402-7 (2006)
Reference
PMID:16922367
  Authors
Tokunaga F.
  Title
[E2 ubiquitin-conjugating enzymes: structures and functions]
  Journal
Tanpakushitsu Kakusan Koso 51:1150-6 (2006)
Reference
PMID:16816840
  Authors
Nalepa G, Rolfe M, Harper JW.
  Title
Drug discovery in the ubiquitin-proteasome system.
  Journal
Nat Rev Drug Discov 5:596-613 (2006)
DOI:10.1038/nrd2056
Reference
PMID:16405856
  Authors
Hsu YJ, Goodman SR.
  Title
Spectrin and ubiquitination: a review.
  Journal
Cell Mol Biol (Noisy-le-grand) Suppl 51:OL801-7 (2005)
Reference
PMID:12944364
  Authors
Hatakeyama S, Nakayama KI.
  Title
Ubiquitylation as a quality control system for intracellular proteins.
  Journal
J Biochem 134:1-8 (2003)
DOI:10.1093/jb/mvg106
Reference
PMID:17588513
  Authors
Lee J, Zhou P.
  Title
DCAFs, the missing link of the CUL4-DDB1 ubiquitin ligase.
  Journal
Mol Cell 26:775-80 (2007)
DOI:10.1016/j.molcel.2007.06.001
Related
pathway
dre03050  Proteasome
KO pathway
ko04120   

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