USP7 - 3D Mechanism Simulator

Loading structural data… (1NBF)

References & Databases

START HERE — how to read Ub-Xaa isopeptide + H₂O → free ubiquitin + Xaa on USP7 A single deubiquitylation cartoon on the human USP7 frame that exists: 1NBF (2.30 Å), chains A/B/E = USP7 catalytic core (UniProt Q93009) and chains C/D = ubiquitin aldehyde. The deposited occupancy is a ubiquitin-aldehyde thiohemiacetal at Cys223 (GLZ C⋯SG ≈ 1.9 Å) — not the substrate isopeptide and not free ubiquitin. Cys223 ★ is the nucleophile; His464/Asp481 the triad; Asn218/Thr222 the oxyanion hole. The Ub-Xaa isopeptide, N/C fragments, E~Ub thioester, water, and transferring H⁺/nucleophile spheres are [schematic]. Blue is the Cys223-SG nucleophile, not a hydride. Gold H⁺ leaves water. Measured Å are deposited 1NBF protein/ligand pairs only. Overlay isopeptide distances are not geomClaims. Chain E USP7 and chain D ubiquitin are copies, not this mesh. Not a pure A-page (E~Ub covalent).
Crystal structures PDB 1NBF — human USP7 (HAUSP) catalytic domain bound to ubiquitin aldehyde, 2.30 Å (Hu 2002). Coordinates are public. Chain B = USP7 UniProt Q93009; chain C = ubiquitin aldehyde (C-terminal Gly aldehyde, ligand GLZ). EC 3.4.19.12 is the current number for ubiquitinyl hydrolase 1; the 1NBF deposition still annotates the older EC 3.1.2.15 (renumbered).
Mechanism — Cys223 cysteine protease, thioester, water hydrolysis USP7 is a ubiquitin-specific protease: Ub-Xaa isopeptide + H₂O → free ubiquitin + Xaa (EC 3.4.19.12). Cys223 SG attacks the isopeptide carbonyl; a covalent E~Ub thioester forms; water then hydrolyses E~Ub. Hu et al., Cell 2002, PMID:12507430. UniProt Q93009 nucleophile is Cys223; His464/Asp481 the catalytic triad. Product teaching = free ubiquitin (Gly76 carboxylate) + Xaa. Source: Hu 2002 · UniProt Q93009
0 — Setup: ubiquitin-aldehyde thiohemiacetal 1NBF holds a ubiquitin-aldehyde thiohemiacetal at Cys223 (Cys223 SG⋯GLZ C ≈ 1.9 Å). That occupancy is the aldehyde adduct, not the substrate isopeptide and not free ubiquitin. Opaque, no autoplay. Chemistry below uses a schematic Ub-Xaa isopeptide. Chain E / chain D are copies.Source: PDB 1NBF
① — Ub-Xaa isopeptide presented A short Ub-Xaa isopeptide docks as a named stand-in for the substrate — [schematic], not the crystal aldehyde and not free ubiquitin. The scissile isopeptide carbonyl (ubiquitin Gly76) faces Cys223 SG. Overlay isopeptide Å are not geomClaims.Source: compiled DUB substrate identity · UniProt Q93009
② — Cys223 attacks C → covalent E~Ub (hypothetical, lit.-based) Blue nucleophile rides from Cys223 SG to isopeptide C. Intact isopeptide fades in place to schematic Ub thioester + Xaa (leaving amine). His464/Asp481 are the triad. Overlay Å are not geomClaims. Slow-motion on purpose. Not a pure A-page.Source: compiled cysteine-DUB · UniProt Q93009
③ — Xaa leaves (hypothetical, lit.-based) Schematic Xaa (the substrate lysine amine) departs. E~Ub thioester stays on Cys223 SG. DUB teaching = the isopeptide opened; ubiquitin still acylated to the enzyme.Source: EC 3.4.19.12 net accounting
④ — Water hydrolyses E~Ub (hypothetical, lit.-based) A schematic water glides in to the E~Ub face. A gold H⁺ leaves water H2 on the yellow arrow and vanishes right at the arrow tip; the remaining OH⁻ attacks E~Ub and its O becomes the ubiquitin Gly76 carboxylate, leaving bound to the product (red ball) — water O is kept, not deleted. The thioester is hydrolysed. Overlay hydrolysis Å are not geomClaims.Source: compiled cysteine-DUB hydrolysis · UniProt Q93009
⑤ — Free ubiquitin leaves — Cys223 restored [schematic] Ubiquitin (Gly76 carboxylate) departs; Cys223 is restored. Product teaching = free ubiquitin + Xaa. The crystal aldehyde was occupancy, not this chemistry. Chain E / chain D are copies, not this mesh.Source: EC 3.4.19.12 net accounting

How to read this page — a first-pass primer First pass: Setup (ubiquitin-aldehyde thiohemiacetal, Cys223 ★) → ① Ub-Xaa isopeptide docks → ② blue SG → C, isopeptide becomes Ub thioester + Xaa → ③ Xaa leaves → ④ gold H⁺ then OH⁻ attacks E~Ub → ⑤ free ubiquitin leaves; Cys223 restored. Second pass: 1.86 / 3.67 / 2.68 / 3.41 / 3.09 / 2.45 Å are crystal facts on 1NBF atoms; isopeptide, fragments, E~Ub, water, and H spheres are [schematic]. Third pass: open “Disagreements” for aldehyde ≠ isopeptide ≠ free ubiquitin, E~Ub covalent, and chain E / chain D as copies.
Chemistry primer — ubiquitin-specific cysteine protease USP7 removes ubiquitin from a Ub-Xaa isopeptide via a Cys223 thioester, then water hydrolyses E~Ub. Gold = H⁺. Blue = Cys223-SG nucleophile (not a hydride). Teaching substrate = Ub-Xaa isopeptide. This is not an E1/E2/E3 cascade and not a proteasome cut.
Words used on screen — occupancy · aldehyde · isopeptide · thioester Occupancy — the crystal holds a ubiquitin-aldehyde thiohemiacetal at Cys223; never relabeled as the substrate isopeptide or free ubiquitin. Aldehyde — the C-terminal Gly76 aldehyde of ubiquitin (GLZ). Isopeptide — the Gly76-ε-amino-lysine link the enzyme actually cleaves (schematic here). Thioester — the covalent E~Ub acyl-enzyme intermediate.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 1NBF (2.30 Å) human USP7 chain B with ubiquitin aldehyde; Cys223 SG ⋯ GLZ C = 1.86 Å; Cys223 SG ⋯ His464 ND1 = 3.67 Å; His464 NE2 ⋯ Asp481 OD1 = 2.68 Å; Asn218 ND2 ⋯ GLZ O = 3.41 Å; Thr222 N ⋯ GLZ O = 3.09 Å; Cys223 N ⋯ GLZ O = 2.45 Å. The inferred layer ([schematic]): Ub-Xaa isopeptide, N/C fragments, E~Ub thioester, water, transferring H⁺/nucleophile spheres, product leave, and capture/hydrolysis split. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Overlay isopeptide contacts are not geomClaims.
Disagreements on record (a) Ubiquitin aldehyde ≠ substrate isopeptide ≠ free ubiquitin. Occupancy is the thiohemiacetal. (b) E~Ub is covalent — not a pure A-page. (c) Isopeptide ≠ this crystal ligand. The aldehyde is a model occupancy; the physiological substrate is a real Ub-Lys isopeptide. (d) Capture vs hydrolysis split. Compiled cysteine-DUB chemistry writes two events; this page plays five beats. (e) Chain E is an isolated USP7 copy, not this mesh. (f) Chain D is a ubiquitin copy, not this mesh. (g) EC renumber. 1NBF annotates 3.1.2.15; current is 3.4.19.12. (h) No protein-domain swing. (i) p53/MDM2 is USP7 Regulation, not motion.
Regulation — p53/MDM2 · HAUSP partners p53/MDM2 deubiquitylation is a physiological role of USP7, named context — not a morph on this page. HAUSP is a synonym for USP7 (same gene product). Other USPs are separate enzymes, not this page.Source: UniProt Q93009 · Hu 2002 PMID:12507430
Kinetics scope (no measured timecourse on this page) One deubiquitylation event is drawn, not a steady-state run. Compiled BRENDA values for EC 3.4.19.12 are not re-asserted here — no measured k_cat/K_m on this page [schematic] (qualitative only). Pair with a kinetics chapter.Source: BRENDA EC 3.4.19.12 — no k_cat/K_m re-asserted
Sequence Human USP7 UniProt Q93009 · NCBI Gene 7874. Screen uses 1NBF numbering; nucleophile Cys223.
Simulation map — what you see is what is written Setup = 1NBF ubiquitin-aldehyde thiohemiacetal (opaque, no autoplay). ① Ub-Xaa isopeptide moves in (schematic). ② slow-mo: blue nucleophile SG → C; isopeptide fades to Ub thioester + Xaa. ③ Xaa leaves. ④ water glides in; gold H⁺ flies flat on the yellow arrow and vanishes at the tip as OH⁻ attacks E~Ub, its O riding out as the product carboxylate. ⑤ free ubiquitin leaves; Cys223 restored. Only these events move.
Sources — bibliography of this page S1 — PDB 1NBF: human USP7 + ubiquitin aldehyde, 2.30 Å — public coordinates; measured SG⋯GLZ C = 1.86 Å · SG⋯His464 ND1 = 3.67 Å · His464 NE2⋯Asp481 OD1 = 2.68 Å · Asn218 ND2⋯GLZ O = 3.41 Å · Thr222 N⋯GLZ O = 3.09 Å · Cys223 N⋯GLZ O = 2.45 Å S2 — Hu et al., Cell 2002, PMID:12507430 — USP7/HAUSP + ubiquitin aldehyde crystal structure S3 — Sequence: UniProt Q93009 (human USP7) · NCBI Gene 7874 S4 — Kinetics: BRENDA EC 3.4.19.12 — no k_cat/K_m re-asserted on this page (qualitative)

› Backbones and ligand poses are taken directly from the listed PDB entries, superposed into one common frame. Where no crystalline state exists for a step (e.g., Ub-Xaa isopeptide, N/C fragments, E~Ub thioester, H⁺ flight, product release), the pose is drawn schematically and labeled as such in the narration.

USP7 catalyticubiquitinONH⁺ (gold)nucleophile (blue)