Ubiquitin

From Proteopedia

proteopedia linkproteopedia link

spinqualitylabelsall models Human ubiquitin (green) complex with ubiquitin-conjugating enzyme E2 (grey), 3k9p Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Function Ubiquitin (UBB) is found in almost all cells. It binds to proteins tagging them for destruction in the proteasome. UBB is activated by the UBB-activating enzymes E1, E2 and E3. UBB+1 is a frameshifted mutant of UBB observed in several diseases. A dimer of UBB (DiUBB) is formed by linkage of K48 to the C-terminus of a second UBB molecule. At least 4 UBB molecules are needed to tag a protein for the proteasome[1]. For details see Ubiquitin Structure & Function Ubiquitin salt bridge discussion Ubiquitin chains. Additional Resources See: Ubiquitin Structure & Function for additional information. Disease The UBB-proteasome system deregulation has been implicated in the pathogenesis of many neurodegenerative disorders like Alzheimer's disease, Parkinson disease, Huntington disease, Prion-like lethal disorders and in genetic diseases like cystic fibrosis, angelman's syndrome, Liddle syndrome and many cancers[2].

3D Structures of Ubiquitin

Updated on 16-November-2017 {{#tree:id=OrganizedByTopic|openlevels=0|

• Ubiquitin

• • 2kn5, 2klg, 2jzz, 2pe9, 2pea, 1g6j, 1d3z, 2kox, 2ld9, 2k25, 5ujl – hUBB – NMR - human
    
  • 2ojr, 2nr2, 2fcq, 1ubi, 1ubq, 1xqq, 3ons, 4wzp, 5k9p, 4zqs, 5dk8, 4xof, 4xok, 4xol, 4zpz - hUBB
    
  • 2zcb, 2gbj, 2gbk, 2gbm, 2gbn, 2gbr, 2fcm, 2fcn, 2fcs, 1yiw, 1yj1, 1sif, 1ogw, 4hk2, 4hjk, 4pij, 4pih, 4pig - hUBB (mutant)
    
  • 1c3t, 1ud7, 2mi8, 2rsu, 2ru6 - hUBB (mutant) - NMR
    
  • 2m0x - hUBB - engineered – NMR
    
  • 1gjz, 2l3z – hUBB N-terminal – NMR
    
  • 1e0q - hUBB N-terminal (mutant) – NMR
    
  • 3q3f – hUBB/ribonuclease
    
  • 4zpz – hPolyUBB-B (mutant)
    
  • 5af4, 4xyz – hPolyUBB-C
    
  • 5af5 – hPolyUBB-C (mutant)
    
  • 2k39 – UBB – Xenopus laevis – NMR
    
  • 2jwz, 1zw7 – yUBB (mutant) – yeast
    
  • 1cmx – yUBB (modified)
    
  • 2zcc – bUBB - bovine
    

• Ubiquitin+1 mutant

• • 2kx0 – hUBB+1 – human – NMR
    
  • 3k9o – hUBB+1+E2
    

• Ubiquitin dimer

• • 2xk5, 3nob, 2xew, 3h7p, 3h7s, 2w9n, 2jf5, 3ns8, 3aul, 3axc, 5gob, 5goc, 5god, 5gog, 5goh, 5goi, 5goj, 5j8p – hDiUBB
    
  • 2mbo, 2mbq – hDiUBB – NMR
    
  • 3m3j, 1aar, 3aui – bDiUBB
    
  • 2bgf – hDiUBB – chemical relaxation
    
  • 4s22 – bDiUBB
    

• Ubiquitin dimer bound to protein

• • 3a9j, 3a9k, 2wwz, 2wx0, 2wx1 – hDiUBB+mitogen-activated protein kinase
    
  • 3jsv, 2zvn, 2zvo – hDiUBB+NF-κ-b essential modulator
    
  • 2kde, 2kdf – DiUBB+26S proteasome non-ATPase regulatory subunit – NMR
    
  • 3a1q – mDiUBB+UBB interaction motif-containing protein
    
  • 3dvg, 3dvn – hDiUBB+IGG1 fab light&heavy chains
    
  • 2znv – mDiUBB+hAMSH-like protease
    3ptf – hDiUBB + UBB conjugating enzyme E2
    
  • 3b08, 3b0a – hDiUBB + HOIL-1
    
  • 3u30 – hDiUBB + antibody
    
  • 4hxd – hDiUBB + RNA polymerase
    
  • 5o6t – hDiUBB + E3 UBB protein ligase XIAP
    
  • 2lvp, 2lvq – hDiUBB + E3 UBB protein ligase - NMR
    
  • 4ksk, 4ksl – hDiUBB + Fam105B
    
  • 4fjv – hDiUBB + UBB thiolesterase
    
  • 4bos – hDiUBB + UBB thiolesterase + OTUD2
    
  • 4s1z – hDiUBB + ZranB1
    
  • 5e6j – hDiUBB (mutant) + replicase polyprotein
    
  • 2n13 – hDiUBB + myosin peptide - NMR
    
  • 3wwq – hDiUBB + FAAP20 peptide
    
  • 5ohp, 5ohn, 5ohk – hDiUBB + USP30
    

• Ubiquitin trimer

• • 5go7, 5gok, 5jby, 5jbv – hTriUBB
    
  • 3zlz, 5o44 – hTriUBB (mutant)
    
  • 4boz – hTriUBB + UBB thiolesterase
    
  • 3vuw, 3vux, 3vuy – hTriUBB + TNF α-induced proitein
    

• Ubiquitin tetramer

• • 5go8 – hTetraUBB
    
  • 3tmp – hTetraUBB + deubiquitinase
    
  • 3alb, 3hm3, 2o6v, 1f9j, 1tbe – tetra-hUBB
    
  • 3zni – hTetraUBB + E3 UBB protein ligase + tyrosine protein kinase + UBB conjugating enzyme E2
    
  • 5b83 – hTetraUBB + optineurin
    

• Polyubiquitin

• • 4zpz – hPolyUBB-B (mutant)
    
  • 5af4, 4xyz – hPolyUBB-C
    
  • 5af5, 5nl4 – hPolyUBB-C (mutant)
    
  • 5x3o, 3x3m – hPolyUBB-B + d-ubiquitin
    
  • 3phd – hPolyUBB+histone deacetylase 6
  • 3znh – hPolyUBB-B + UBB thioesterase
    
  • 4uf6 – hPolyUBB-B + UCH-L5 + NF-κ-b-related protein
    
  • 5vf0 – hPolyUBB-B + RAD18 - NMR
    
  • 5vey – hPolyUBB-B + RNF169 + Histone H2A-H2B - NMR
    
  • 5n38 , 5n2w – hPolyUBB-B + E3 UBB protein ligase PARKIN
    
  • 5mnj – hPolyUBB-B + E3 UBB protein ligase MDM2 + UBCH5B
    
  • 5l8w – hPolyUBB-B + WD repeat-containing protein 48 + USP12
    
  • 5l8h – hPolyUBB-B + WD repeat-containing protein 48 + USP46
    
  • 5kyf, 5kye, 5kyd, 5kyc – hPolyUBB-B + USP7
    
  • 3znz – hPolyUBB-C + otulin
    
  • 4jqw – hPolyUBB-C + NOD1 CARD
    
  • 4k1r – hPolyUBB-C + SST2
    
  • 5oe7 – hPolyUBB-C + otulin
    

• Ubiquitin monomer bound to protein

• • 3ofi – hUBB+insulin protease
  • 3n3k, 3ifw, 3kvf, 3kw5, 3irt, 3mtn, 3ihp, 3v6c, 3v6e– hUBB (mutant)+hUBB carboxyl-terminal esterase catalytic domain
    
  • 3i3t, 2ibi, 2ayo, 1nbf, 2wdt, 4i6l, 4i6n, 4ig7, 5l8h, 5jtj, 5cvm - hUBB+hUBB carboxyl-terminal hydrolase catalytic domain
    
  • 5l8w, 5cvn, 5cvo – hUBB + UBB carboxy terminal hydrolase 12 + WD repeat containing protein 48
    
  • 2khw – hUBB+immunoglobulin G-binding protein G
    
  • 1yx5, 1yx6 - hUBB+26S proteasome non-ATPase regulatory subunit – NMR
    
  • 2k6d – hUBB+SH3 domain-containing kinase-binding protein – NMR
    
  • 2z59 – hUBB+mProtein Adhesion-regulating molecule 1
    
  • 2jy6 – hUBB+hUbiquilin – NMR
    
  • 3by4, 3c0r – hUBB+yUBB thioesterase
    
  • 2hth – hUBB+vacuolar protein sorting protein
    
  • 1s1q – hUBB+tumor susceptibility gene 101 protein
    
  • 1q5w – hUBB+NPL4 zinc-fingers
    
  • 2k8b, 2k8c – hUBB+phospholipase A2-activating protein fragment
    
  • 2ktf – hUBB+hDNA polymerase IOTA
    
  • 2l0f – hUBB (mutant)+hDNA polymerase IOTA
    
  • 2kwu, 2kwv - hUBB+mDNA polymerase IOTA – mouse
    
  • 2l0t – hUBB+signal transducing adapter molecule 2
    
  • 3o65 – hUBB+ataxin-3-like protein josephin domain
    
  • 3oj3 – hUBB+tumor necrosis factor -induced protein 3
    
  • 3phd – hPolyUBB+histone deacetylase 6
    
  • 3znh – hPolyUBB-B + UBB thioesterase
    
  • 4uf6 – hPolyUBB-B + UCH-L5 + NF-κ-b-related protein
    
  • 3znz – hPolyUBB-C + otulin
    
  • 4jqw – hPolyUBB-C + NOD1 CARD
    
  • 4k1r – hPolyUBB-C + SST2
    
  • 3prm, 3prp – hUBB+protein L
    
  • 3pt2 – hUBB+RNA polymerase OTU domain
    
  • 5v5i, 5v5h, 5v5g - hUBB+RNA polymerase L
    
  • 2rr9 – hUBB + Uimc1
    
  • 1fxt, 3oj4, 3ugb, 5dfl, 3k9p, 3a33 – hUBB + UBB conjugating enzyme E2
    
  • 2fuh – hUBB + UBB conjugating enzyme E2 - NMR
    
  • 4auq – hUBB + UBB conjugating enzyme E2 + livin
    
  • 2g45 – hUBB + isopeptidase T
    
  • 2den – hUBB + immunoglobulin G binding protein/ubiquitin-like protein 7 - NMR
    
  • 2oob, 2qho – hUBB + E3 UBB protein ligase
    
  • 2lvo – hUBB + E3 UBB protein ligase - NMR
    
  • 2j7q – hUBB + MCMV tegument protein
    
  • 4dhj, 4dhz – hUBB (mutant) + UBB thiolesterase + UBB aldehyde
    
  • 3rul – hUBB + dalvancin
    
  • 3vfk – hUBB + monodechloro-teicoplanin
    
  • 4ium, 4wur, 4mm3 – hUBB+ papain-like protease
    
  • 2lz6, 2mcn – hUBB + CD2-associated protein
    
  • 2mbh – hUBB + Kreuppel-like factor
    
  • 3tbl – hUBB + PCNA
    
  • 3vht – hUBB + GFP
    
  • 4jio – hUBB + yBRO1
    
  • 5af6 – hUBB + TRABID
    
  • 4un2 – hUBB + Dsk2 peptide
    
  • 4msq, 4msm – hUBB + AMSH-like protease
    
  • 5ln1 – hUBB + RPN10
    
  • 5v1z, 5v1y – hUBB + RPN13 + RPN2
    
  • 5jp3 – hUBB + xanthomonas outer protein
    
  • 5lrw – hUBB (mutant)+ OUT domain containing protein 7B
    
  • 5lrx – hUBB (mutant)+ OUT domain containing protein 7C
    
  • 5kgf – hUBB + nucleosome - Cryo EM
    
  • 2nbv – hUBB + proteasomal UBB receptor - NMR
    
  • 5jg6 – hUBB + anaphase promoting complex subunit 11
    
  • 6eqi – hUBB + NB696 + PINK1
    
  • 5ohv – hUBB + K33-specific affimer
    
  • 5af6 – hUBB + TRABID
    
  • 4un2 – hUBB + Dsk2 peptide
    
  • 4msq, 4msm – hUBB + AMSH-like protease
    
  • 4m0w – bUBB + replicase polyprotein
    
  • 1uzx – bUBB+VPS23 UEV
    
  • 2hd5 - bUBB+hUBB carboxyl-terminal hydrolase catalytic domain
    
  • 3ldz – bUBB+signal transducing adapter molecule
    
  • 1v80, 1v81 – bUBB/L40 ribosomal protein fusion - NMR
    
  • 2dx5, 1p3q - bUBB+vacuolar protein sorting protein
    
  • 2c7m, 2c7n, 2fid, 2fif – bUBB+RAB guanine nucleotide exchange factor
    
  • 2d3g – bUBB+HRS-UIM
    
  • 1wrd – bUBB+TOM1 GAT domain
    
  • 1wr6, 1yd8 - bUBB+GGA3 GAT domain
    
  • 1uzx – bUBB+VPS23 UEV
    
  • 2kdi – yUBB/UIM fusion
    
  • 2jt4 – yUBB fragment+cytoskeleton assembly control protein
    
  • 1q0w - yUBB+vacuolar protein sorting protein
    
  • 2g3q – yUBB+EDE1 UBA
    
  • 1wr1 – yUBB+DSK2P UBA
    
  • 1otr – yUBB+CUE2
    
  • 2l00 – yUBB + Zfand5
    
  • 4q5h, 4q5e – yUBB + UBB conjugating enzyme E2 + OspG
    
  • 4nql – mUBB + AMSH-like protease
    

• Ubiquitin complex with ubiquitination enzymes

• • 1fxt, 3oj4, 3ugb, 5dfl, 3k9p, 3a33, 5ulf, 5tut – hUBB + UBB conjugating enzyme E2
    
  • 5bnb, 2kjh, 1zgu – hUBB (mutant) + UBB conjugating enzyme E2
    
  • 5edv, 4whv, 5ait, 5aiu, 3jvz, 3jw0, 5udh, [[5tte] – hUBB + UBB conjugating enzyme E2 + E3 UBB-protein ligase
    
  • 3cmm – yUBB + UBB activating enzyme E1
    
  • 5knl – yUBB (mutant) + UBB activating enzyme E1 + UBB conjugating enzyme E2
    
  • 5tr4 – bUBB + UBB activating enzyme E1
    
  • 2gmi – hUBB + UBB conjugating enzyme E2
    
  • 5d0k, 5d0m, 5ulk, 5ulh – hUBB + UBB conjugating enzyme E2 + RNF165
    
  • 4xkl – hUBB + NDP52
    
  • 4zfr, 4zft – hUBB + SST2
    
  • 5o76 – hUBB + Zap70 peptide + E3-UBB-protein ligase CBL
    
  • 2fuh – hUBB + UBB conjugating enzyme E2 - NMR
    
  • 4auq – hUBB + UBB conjugating enzyme E2 + livin
    
  • 4q5h, 4q5e – yUBB + UBB conjugating enzyme E2 + OspG
    

• Ubiquitin + ions

• • 3h1u – bUBB+Cd
    
  • 3ehv, 3eec, 3efu – hUBB+ions
    
  • 3n30, 4k7s, 4k7u, 4k7w – hUBB+Zn
    
  • 3n32 – hUBB+Pt
    

}}

References

1. ↑ Hershko A, Ciechanover A. The ubiquitin system. Annu Rev Biochem. 1998;67:425-79. PMID:9759494 doi:http://dx.doi.org/10.1146/annurev.biochem.67.1.425
2. ↑ Paul S. Dysfunction of the ubiquitin-proteasome system in multiple disease conditions: therapeutic approaches. Bioessays. 2008 Nov;30(11-12):1172-84. doi: 10.1002/bies.20852. PMID:18937370 doi:http://dx.doi.org/10.1002/bies.20852