1. The Diversity of Ubiquitin Recognition: Hot Spots and Varied Specificity 
Jason M. Winget, Thibault Mayor 
Molecular Cell 
Volume 38, Issue 5, Pages (June 2010)
DOI: /j.molcel
Copyright © 2010 Elsevier Inc. Terms and Conditions

2. Figure 1 Interactions with Ubiquitin
(A) Backbone fold of ubiquitin, with secondary structure elements labeled.
(B) Selected residues on ubiquitin are rendered as sticks and labeled.
(C) The surface of ubiquitin, colored by residue type. The color scheme is gray for nonpolar, green for polar (uncharged), red for acidic, and blue for basic. Regions of binding as described in the text are indicated.
(D) A heat map of reported interactions based on chemical shift potentials shows that the hydrophobic patch is a binding hot spot. Data used for this map are shown in Figure S1A. Residues with few interactions are yellow; residues with many interactions are red. Those with none are gray. Chemical shift data may not capture all of the interactions involved in binding.
(E and F) “Footprints” on ubiquitin based on residues within 4 Å of the UBD: the footprint (red) of UBA (Dsk2) binding on the ubiquitin surface from PDB structure 1WR1 (E) and UIM (S5a) binding footprint, as in (E), from PDB 1YX5 (F). Full structures for these and other selected UBDs are shown in Figure S1.
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3. Figure 2
UBL Proteins Bind Partners via an Expansion of the Hydrophobic Patch
(A) Sequences for the UBLs discussed in the text were aligned with MUSCLE (Edgar, 2004). The UBL/UBD pair is listed to the left. Reported UBL/UBD contacts based on NMR chemical shifts are shaded. Sequence similarity is indicated below the alignment by asterisks for identical, colons for highly similar, and periods for somewhat similar residues. Unique UBLs were weighted evenly during calculation of the similarity. Secondary structural elements of ubiquitin are shown as blue arrows for β strands and red cylinders for helices. Surface-exposed residues within 8 Å of the ubiquitin Ile44 Cβ are indicated by arrowheads.
(B) Yeast Rpn10 interactions with Dsk2 UBL (PDB 2BWF; as listed in A) are colored red on the UBL surface, oriented as in Figure 1. Ile44 is indicated by an asterisk.
(C) Murine Parkin UBL interactions with Endophilin A, mapped onto human Parkin as in (B). The PxRK extension (indicated by the arrow) is underlined in (A), bottom row.
(D) Human Parkin UBL (PDB 1IYF) interactions with Eps15, as in (B).
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4. Figure 3 Interactions at the α1/β2 Groove Are Electrostatic in Nature
(A) The location of the α/β groove is shown by comparison to the C terminus of SUMO1. The surface of SUMO1 with the bound SIM1 displayed in yellow is shown to the right, in the same orientation as the adjacent backbone cartoon.
(B–F) Electrostatic surfaces for proteins mentioned in the text that undergo binding to partners via the α/β groove, in the same orientation as the SUMO1 surface in (A): SUMO1 (B), LC3 (C), Elongin B (D), Ring1B (E), and ubiquitin (F). Despite differences in surface topology, the core backbone folds of the domains shown are very similar. Charges were assigned at pH 7, and continuum electrostatics were calculated with APBS (Baker et al., 2001). PDB codes are 2ASQ, 2K6Q, 1VCB, 3H8H, and 1UBQ, respectively.
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5. Figure 4 Different Mechanisms of Polyubiquitin Recognition
(A–D) Residues on the polyubiquitin chain within 4 Å of the interacting partner are colored red. The ubiquitin linkage is colored yellow (or orange if included in the interaction). Insets show cartoon for orientation, with the proximal and distal ubiquitin moieties indicated. Shown are AMSH DUB bound to Lys63-linked diubiquitin (A), NEMO CoZi domain bound to linear diubiquitin (B), modeled major conformation of S5a with Lys48-linked diubiquitin (C), and TAB2 bound to Lys63-linked diubiquitin (D). PDB codes are 2ZNV, 2ZVO, 2KDE, and 2WWZ, respectively.
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6. Figure 5 Schematics of Ternary Complexes
(A) Rad23A and S5a can bind tetraubiquitin simultaneously via their respective UBDs, and the other UIM domain of S5a can then interact with the UBL of Rad23A.
(B) Rpn13 can bind to the proximal ubiquitin, causing S5a UIM domains to compete with one another for binding to the distal ubiquitin.
(C) In short ubiquitin chains, Rpn10 interacts with the UBL of Dsk2, while Dsk2 binds polyubiquitin via its UBA domain. In longer chains, Rpn10 binds directly to polyubiquitin, unmasking the Dsk2 UBL for potential targeting to the proteasome.
Molecular Cell  , DOI: ( /j.molcel )
Copyright © 2010 Elsevier Inc. Terms and Conditions