Structural basis for assembly and activation of the heterotetrameric SAGA histone H2B deubiquitinase module

Abstract

Deubiquitinating enzymes (DUBs) regulate diverse cellular functions by cleaving ubiquitin from specific protein substrates. How their activities are modulated in various cellular contexts remains poorly understood. The yeast deubiquitinase Ubp8 protein is recruited and activated by the SAGA complex and, together with Sgf11, Sus1, and Sgf73, forms a DUB module responsible for deubiquitinating histone H2B during gene expression. Here, we report the crystal structure of the complete SAGA DUB module, which features two functional lobes structurally coupled by Sgf73. In the "assembly lobe," a long Sgf11 N-terminal helix is clamped onto the Ubp8 ZnF-UBP domain by Sus1. In the "catalytic lobe," an Sgf11 C-terminal zinc-finger domain binds to the Ubp8 catalytic domain next to its active site. Our structural and functional analyses reveal a central role of Sgf11 and Sgf73 in activating Ubp8 for deubiquitinating histone H2B and demonstrate how a DUB can be allosterically regulated by its nonsubstrate partners.

Figure 1. Overall view of the yeast SAGA DUB module

(A) Two orthogonal views of the complex. Ubp8 (blue), Sgf11(red), Sus1 (green), and Sgf73 (orange) are shown in ribbon representation with disordered regions in dashed lines. The zinc ions are shown as yellow spheres. The active site cysteine is shown in cyan CPK model. (B) Individual or different combination of the DUB module subunits are shown in surface representation to demonstrate their spatial relationships. The orientation of all subunits is the same as shown in (A, left). See Table S1 for crystallographic information.

Figure 2. The Ubp8 ZnF-UBP domain mediates complex assembly of the DUB module

(A) Superposition analysis of the ZnF-UBP domains in Ubp8 (blue) and USP5 (grey). The three zinc ions in the Ubp8 ZnF-UBP domain are numbered (yellow spheres). Secondary structure elements of both proteins are labeled (H for α-helix and S for βstrand). (B) The ubiquitin tail-binding pocket of the USP5 ZnF-UBP domain. The side chains of key ubiquitin-contacting residues in USP5 and the last three ubiquitin residues are shown in sticks. (C) The corresponding region of Ubp8 as shown for USP5 in (B). The side chains of key residues from Ubp8, Sus1, and Sgf11 for forming a three-protein junction are shown in sticks. (D) and (E) Two views of the entire “assembly lobe” of the DUB module. (F) The interface between the Ubp8 ZnF-UBP domain and the second helix of Sgf73 featuring the conserved WK motif. The side chains of the Sgf73 WK motif are shown in sticks. The Ubp8 ZnF-UBP domain is shown in surface representation. The two backbone carbonyl groups of Ubp8, which accept hydrogen bonds from the Sgf73 WK motif are colored in red. (G) The indicated DUB module components were polycistronically expressed in E. coli. Protein lysates were split and subjected in parallel to either GST- or 6His-affinity purifications. Lanes 1 and 4, 2 and 5, 3 and 6 correspond to each other. Purified complexes were eluted with either GSH or imidazole and analyzed by SDS-PAGE and Coomassie staining. Filled circles indicate bait proteins. Labeled proteins were identified by mass spectrometry. See also Figure S1.

Figure 3. Sus1 clamps down the Sgf11 N-terminal helix onto the Ubp8 ZnF-UBP domain

(A) Overall view of the “assembly lobe” in the DUB module. (B) A three-protein junction formed among the two terminal helices of Sus1 (green) and the N-terminal end of Sgf11 (red) and Sgf73 (orange). (C) Superposition analysis of Sus1 in complexes with Sgf11 (red) and Sac3 (magenta). The Sus1 molecule in the Sus1-Sgf11 and Sus1-Sac3 complexes is colored in green and grey, respectively. The Cα of Sus1-contacting residues in Sgf11 and Sac3 are labeled with asterisks. (D) and (E) Two orthogonal views of the superimposed Sus1-Sgf11 and Sus1-Sac3 complex structures. H2 and H5 helices of Sus1 in the two structures were superimposed to demonstrate the structural plasticity of Sus1. (F) Reconstitution assay with recombinant proteins. GST-Ubp8 (1–107) was immobilized on GSH beads (filled circle) and incubated with either Sus1 or Sgf11 alone or with equal molar amounts of both proteins (input).

Figure 4. The Sgf11 ZnF domain binds to the Ubp8 catalytic domain next to the active site

(A) Overall view of the “catalytic lobe” of the SAGA DUB module. The Ubp8 catalytic domain is differentially colored to show the three sub-domains, Thumb (grey), Palm (blue), and Fingers (cyan). The catalytic triad of Ubp8 are shown in sticks. (B) A close-up view of the Ubp8 active site with the catalytic triad (C146, H427, and N443) and two amino acids (N141 and D444) that might help stabilize the oxyanion hole. (C) Interface between the Sgf11 ZnF domain and the Ubp8 Thumb domain. The three conserved arginine residues exposed at the outer surface of the Sgf11 ZnF domain are also shown. (D) Interface between the Sgf11 linker sequence and the Palm domain within the Ubp8 catalytic domain. The Ubp8 catalytic triad, the two Sgf11 DxxG motifs, and their surrounding residues are shown in sticks. (E) Sequence alignment of Sgf11 orthologs with secondary structure assignment. The zinc-coordinating residues are highlighted in yellow. Other highly conserved residues are highlighted in salmon. See also Figure S2.

Figure 5. The Sgf11 ZnF domain activates Ubp8 and mediates Ub-H2B deubiquitination

(A) and (B) Ub-AMC hydrolysis assay. Coomassie staining shows equalized amount of Ubp8 and overall composition of the complexes. (C) In vitro H2B deubiquitination assay. Hyperubiquitinated Flag-tagged H2B purified from ubp8Δ cells was incubated with equal amounts of the indicated wild-type and mutant DUB tetramers as depicted in (A) and (B). Ubiquitinated and unmodified H2B were detected by anti-Flag western blotting. (D) Anti-Flag immunoprecipitates derived from cells expressing Flag–tagged H2B. sgf11Δ cells were transformed with plasmids carrying the indicated wild-type, mutant sgf11 alleles or an empty vector. Recovered proteins were analyzed by SDS–PAGE and anti-Flag western blotting. (E) A GCN5/sgf11Δ shuffle strain containing a GCN5 cover plasmid (URA3) was transformed with wild-type SGF11, empty vector or the indicated sgf11 mutant alleles (TRP1 plasmids). Growth was followed on SDC-Trp and on SDC+5-fluoroorotic acid (5-FOA) plates. Cell density was normalized, cells were spotted onto plates in 10-fold serial dilution steps and incubated at 30°C for 2 days (SDC-TRP) and 4 days (SDC+5-FOA). See also Figure S3 and Table S2 for yeast strains and plasmids used.

Figure 6. Sgf73 couples the two functional lobes of the DUB module and potentiates Ubp8

(A) A close-up view of the space between the two Ubp8 domains occupied by Sgf73. The structure is depicted in the same orientation as seen in Figure 1B. Sgf73 is shown in ribbon with the rest of the DUB complex shown in surface representation. (B) Left side view of (A) showing that the H2-loop-H3 region of Sgf73 holds together the two domains of Ubp8 at one end of the complex. (C) Right side view of (A) showing that the Sgf73 ZnF domain functions as a wedge to fix the conformation of the Ubp8 linker sequence, which is also in contact with the Sgf11 linker region. Key residues of the Sgf11 linker are shown in sticks. Two Ubp8 residues forming salt bridges with two positively charged Sgf11 residues are colored in red. (D) A focused view of the DUB module showing the spatial relationships among the Sgf73 ZnF domain, the Ubp8 linker sequence, the Sgf11 C-terminal region, and the Ubp8 active site. (E) Ub-AMC hydrolysis assay. Coomassie staining shows equalized amount of Ubp8 and overall composition of the complexes (filled circle marks bait proteins). (F) A tetrameric complex containing Sgf73 amino acids 1–47 (lane 3) was preincubated with recombinant Sgf73 amino acids 48–104 at a 1:1 or 1:10 stoichiometry (30° for 15min) and subsequently assayed for Ub-AMC hydrolytic activity. Coomassie-stained gel shows imidazole eluates of affinity-purified 6His-Sgf73 complexes (filled circle). (G) A GCN5/sgf73Δ shuffle strain was transformed with wild-type SGF73, empty vector or the indicated sgf73 mutant alleles (TRP1 plasmids). Growth was followed on SDC-Trp and on SDC+5-fluoroorotic acid (5-FOA) plates. See also Figure S4.

Figure 7

Model for the assembly and activation of the SAGA DUB module. Free Ubp8 (blue) has a ZnF-UBP domain (square) and an inactive catalytic domain (full circle). Independent from other subunits, Sus1 (green) can form a complex with Sgf11 (red) by wrapping around its N-terminal helix (hexagon). The correctly positioned ZnF domains of Sgf11 (red circle) and Sgf73 (orange circle) are both required to fully activate Ubp8 (sharp teeth). See also Figure S5.