Ubiquitin

From Proteopedia

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Template:STRUCTURE 3k9p

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. The images at the left and at the right correspond to one representative Ubiquitin, i.e. the NMR structure of human Ubiquitin (1d3z). For details see

• Ubiquitin Structure & Function
  
• Ubiquitin salt bridge discussion
  
• Ubiquitin chains.

Additional Resources

See: Ubiquitin Structure & Function for additional information.

3D Structures of Ubiquitin

Updated on 29-May-2014

Ubiquitin

2kn5, 2klg, 2jzz, 2pe9, 2pea, 1g6j, 1d3z, 2kox, 2ld9, 2k25 – hUBB – NMR - human
2ojr, 2nr2, 2fcq, 1ubi, 1ubq, 1xqq, 3ons - hUBB
2zcb, 2gbj, 2gbk, 2gbm, 2gbn, 2gbr, 2fcm, 2fcn, 2fcs, 1yiw, 1yj1, 1sif, 1ogw, 4hk2, 4hjk - 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
2k39 – UBB – Xenopus laevis – NMR
2jwz, 1zw7 – yUBB (mutant) – yeast
1cmx – yUBB (modified)
2zcc – bUBB - bovine

Ubiquitin+UBB-activating enzymes

3cmm – yUBB+E1
3k9p, 3a33 – hUBB+E2
2gmi - hUBB+E2+MMS2
2kjh, 1zgu – hUBB (mutant)+E2
3jvz, 3jw0 – hUBB+E2+E3

Ubiquitin+1 mutant

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

Ubiquitin dimer

2xk5, 3nob, 2xew, 3h7p, 3h7s, 2w9n, 2jf5, 3ns8, 3aul, 3axc – hDiUBB
2mbo, 2mbq – hDiUBB – NMR
3m3j, 1aar, 3aui – bDiUBB
2bgf – hDiUBB – chemical relaxation

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
2lvp, 2lvq – hDiUBB + E3 UBB protein ligase - NMR
4ksk, 4ksl – hDiUBB + Fam105B
4fjv – hDiUBB + UBB thiolesterase
4bos – hDiUBB + UBB thiolesterase + OTUD2

Ubiquitin trimer

3zlz – hTriUBB (mutant)
4boz – hTriUBB + UBB thiolesterase
3vuw, 3vux, 3vuy – hTriUBB + TNF α-induced proitein

Ubiquitin tetramer

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

Ubiquitin 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 - hUBB+hUBB carboxyl-terminal hydrolase catalytic domain
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
3znz – hPolyUBB-C + otulin
4jqw – hPolyUBB-C + NOD1 CARD
4k1r – hPolyUBB-C + SST2
3prm, 3prp – hUBB+protein L
3pt2 – hUBB+RNA polymerase OTU domain
2rr9 – hUBB + Uimc1
1fxt, 3oj4, 3ugb – 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 – hUBB+ papain-like protease
2lz6, 2mcn – hUBB + CD2-associated protein
2mbh – hUBB + Kreuppel-like factor
3tbl – hUBB + PCNA
3vht – hUBB + GFP
4jio – hUBB + yBRO1
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

Ubiquitin + ions

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