Ubiquitin

From Proteopedia

Revision as of 13:19, 18 November 2012

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 and Ubiquitin chains.

Additional Resources

See: Ubiquitin Structure & Function for additional information.

3D Structures of Ubiquitin

updated December 2011

Ubiquitin

2kn5, 2klg, 2jzz, 2pe9, 2pea, 1g6j, 1d3z, 2kox, 2ld9 – hUBB – NMR - human
2ojr, 2nr2, 2fcq, 1ubi, 1ubq, 1xqq, 3ons - hUBB
2zcb, 2gbj, 2gbk, 2gbm, 2gbn, 2gbr, 2fcm, 2fcn, 2fcs, 1yiw, 1yj1, 1sif, 1ogw - hUBB (mutant)
1c3t, 1ud7 - hUBB (mutant) - NMR
1gjz, 2l3z – hUBB N-terminal – NMR
1e0q - hUBB N-terminal (mutant) – NMR
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 – hDiUBB
3m3j, 1aar – bDiUBB
2bgf – hDiUBB – chemical relaxation

Ubiquitin tetramer

3alb, 3hm3, 2o6v, 1f9j, 1tbe – tetra-hUBB

Ubiquitin bound to protein

3ofi – hUBB+insulin protease 3n3k, 3ifw, 3kvf, 3kw5, 3irt, 3mtn, 3ihp – hUBB (mutant)+hUBB carboxyl-terminal esterase catalytic domain
3i3t, 2ibi, 2ayo, 1nbf - 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
3prm, 3prp – hUBB+protein L
3pt2 – hUBB+RNA polymerase OTU domain
2rr9 – hUBB + Uimc1
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 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

Ubiquitin + ions

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