PSMD14 - 3D Mechanism Simulator

Loading structural data… (8USB)

References & Databases

START HERE — how to read Ub-Xaa isopeptide + H₂O → free ubiquitin + Xaa on PSMD14 A single deubiquitylation cartoon on the human PSMD14 frame that exists: 8USB (2.73 Å cryo-EM human 26S proteasome, chain V) = PSMD14 / POH1 (UniProt O00487), the 19S-lid JAMM deubiquitinase. The deposited occupancy is the JAMM Zn²⁺ site — Zn coordinated by His113 / His115 / Asp126 / Glu52 — with no substrate, no isopeptide and no water modeled. So the Ub-Xaa isopeptide, the water that docks at Zn (and the hydroxide it becomes), and the N/C fragments are [schematic]. Zn²⁺ is the Lewis acid; Ser123 ★ (JAMM motif) is the schematic general base. This is direct hydrolysis at the Zn site with NO covalent E~Ub — the opposite architecture to the USP7 cysteine DUB, which forms a thioester. Measured Å are deposited 8USB pairs only; overlay isopeptide distances are not geomClaims. Residues 311–312 are a non-native tag scar and are not shown.
Crystal structures PDB 8USB — non-substrate-engaged human 26S proteasome, 2.73 Å cryo-EM (Nub1/FAT10 bound to Rpn1). Coordinates are public. Chain V (entity 22) = PSMD14 UniProt O00487; entity 31 = the single deposited JAMM Zn²⁺. EC 3.4.19.12 (ubiquitinyl hydrolase) — PSMD14 is a metallo deubiquitinase, not a cysteine protease.
Mechanism — JAMM Zn²⁺ metalloprotease, direct hydroxide attack PSMD14 / RPN11 removes ubiquitin from a Ub-Xaa isopeptide: Ub-Xaa isopeptide + H₂O → free ubiquitin + Xaa. A water at the Zn²⁺ site is deprotonated, and the resulting hydroxide attacks the isopeptide carbonyl in a single direct hydrolysis (NO covalent enzyme intermediate). Zn²⁺ = Lewis acid; Ser123 (JAMM motif) is the schematic general base. UniProt O00487 annotates the JAMM Zn-binding residues His113 / His115 / Asp126. Source: UniProt O00487 · PDB 8USB
0 — Setup: JAMM Zn²⁺ active site 8USB holds the JAMM Zn²⁺ coordinated by His113 / His115 / Asp126 / Glu52, open toward Ser123. 8USB models no substrate, no isopeptide and no water. Opaque, no autoplay. The chemistry below is schematic. Residues 311–312 are a non-native tag scar and are not shown.Source: PDB 8USB
① — Ub-Xaa isopeptide presented A short Ub-Xaa isopeptide docks as a named stand-in for the substrate — [schematic], not a modeled state in 8USB and not free ubiquitin. The scissile isopeptide carbonyl (ubiquitin Gly76) is presented to the Zn–Ser123 face. Overlay isopeptide Å are not geomClaims.Source: compiled DUB substrate identity · UniProt O00487
② — Catalytic water docks at Zn (hypothetical, lit.-based) A catalytic water (schematic — 8USB models none) docks into the open Zn²⁺ coordination site next to the base Glu52 ★. Zn²⁺ stays as the Lewis acid. Water is consumed in the cut. Overlay water distances are not geomClaims.Source: UniProt O00487 JAMM motif
③ — Glu52 takes the water proton → hydroxide at Zn (hypothetical, lit.-based) Gold H⁺ leaves water H2 to the conserved Glu52 ★ (schematic general base; also a Zn ligand). The remaining O–H1 is the hydroxide (blue), still sitting at the Zn site. 8USB models no water, so this proton transfer is schematic. No covalent enzyme intermediate.Source: UniProt O00487 JAMM motif
④ — hydroxide attacks C → free ubiquitin + Xaa (hypothetical, lit.-based) The blue hydroxide attacks the isopeptide carbonyl. The intact isopeptide cross-fades to schematic free ubiquitin + Xaa. Single direct hydrolysis, no covalent E~Ub. Overlay Å are not geomClaims. Slow-motion on purpose.Source: compiled JAMM chemistry · UniProt O00487
⑤ — Free ubiquitin + Xaa leave — Zn site restored [schematic] Free ubiquitin (Gly76 carboxylate) and Xaa depart; the JAMM Zn²⁺ and its four protein ligands are restored. Product teaching = free ubiquitin + Xaa with no covalent intermediate. 8USB modeled no substrate; the cut state was schematic. Residues 311–312 are not shown.Source: EC 3.4.19.12 net accounting

How to read this page — a first-pass primer First pass: Setup (JAMM Zn²⁺ site, Ser123 ★) → ① Ub-Xaa isopeptide docks → ② water docks at Zn → ③ gold H⁺ to Glu52, hydroxide forms → ④ blue OH⁻ attacks C, isopeptide → Ub + Xaa → ⑤ products leave; Zn restored. Second pass: 2.30 / 2.30 / 1.93 / 1.96 / 4.10 / 3.56 Å are crystal facts on 8USB atoms; isopeptide, water, hydroxide and fragments are [schematic]. Third pass: open “Disagreements” for JAMM-metallo ≠ cysteine (USP7), no covalent E~Ub, and the tag scar.
Chemistry primer — JAMM Zn²⁺ metalloprotease PSMD14 is a Zn²⁺-dependent deubiquitinase: a water at the Zn site is deprotonated and its hydroxide cuts the isopeptide carbonyl directly — no acyl-enzyme. Gold = H⁺. Blue = hydroxide nucleophile (not a hydride). Teaching substrate = Ub-Xaa isopeptide. This is not an E1/E2/E3 cascade, not a proteasome peptide cut, and not the USP7 cysteine thioester.
Words used on screen — occupancy · JAMM · hydroxide · direct hydrolysis Occupancy — 8USB holds the JAMM Zn²⁺ site with no substrate and no water; never relabeled as a substrate complex. JAMM — the Zn-binding MPN+ motif (His113-His115…Asp126) that defines this metalloprotease family. hydroxide — the water at Zn loses its proton and its OH⁻ becomes the nucleophile (schematic here). Direct hydrolysis — one water attack on the carbonyl with no covalent enzyme intermediate.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 8USB (2.73 Å) human 26S chain V; Zn ⋯ His113 NE2 = 2.30 Å; Zn ⋯ His115 NE2 = 2.30 Å; Zn ⋯ Asp126 OD2 = 1.93 Å; Zn ⋯ Glu52 OE1 = 1.96 Å; Ser123 OG ⋯ Zn = 4.10 Å; Ser123 OG ⋯ Asp126 OD2 = 3.56 Å. The inferred layer ([schematic]): Ub-Xaa isopeptide, the water that docks at Zn (and its hydroxide), N/C fragments, product release, and the proton relay. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Overlay isopeptide contacts are not geomClaims.
Disagreements on record (a) JAMM Zn²⁺ metalloprotease ≠ cysteine DUB. PSMD14 cuts with a hydroxide held at Zn; USP7 uses a Cys thioester. (b) No covalent E~Ub here — the cut is a single direct hydrolysis. (c) 8USB has no substrate and no water — the isopeptide and the nucleophile are schematic. (d) Glu52 contact. 8USB models Glu52 OE1 at 1.96 Å from Zn; whether it is a true inner-sphere ligand or a modelled contact, the catalytic water is not modeled either way. (e) Ser123 general base. Assigned from the JAMM motif and the deposited Zn⋯OG geometry; the relay is schematic. (f) Tag scar. Residues 311–312 are non-native and excluded. (g) EC. UniProt O00487 lists EC 3.4.19.12 (metallo deubiquitinase; evidence PubMed 22909820 / 32210007); the isopeptidase reaction shown is that class. (h) No protein-domain swing.
Regulation — 19S lid · Rpn1/Nub1 context PSMD14 (POH1 / RPN11) is the deubiquitinase of the 19S regulatory particle lid; it removes ubiquitin en bloc during substrate translocation. Nub1/FAT10 bound to Rpn1 is the 8USB context, named — not a morph on this page. Other JAMM enzymes (AMSH, CSN5) are separate enzymes, not this page.Source: UniProt O00487 · PDB 8USB
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 PSMD14 UniProt O00487 · NCBI Gene 10213. Screen uses 8USB UniProt numbering (chain V, 23–310); JAMM Zn-binding residues His113 / His115 / Asp126, motif Ser123.
Simulation map — what you see is what is written Setup = 8USB JAMM Zn²⁺ site (opaque, no autoplay). ① Ub-Xaa isopeptide moves in (schematic). ② water docks at Zn. ③ slow-mo: gold H⁺ to Glu52, hydroxide forms. ④ slow-mo: blue OH⁻ attacks C; isopeptide fades to free ubiquitin + Xaa. ⑤ products leave; Zn restored. Only these events move.
Sources — bibliography of this page S1 — PDB 8USB: human 26S proteasome (non-substrate-engaged), 2.73 Å cryo-EM — public coordinates; measured Zn ⋯ His113 NE2 = 2.30 Å · Zn ⋯ His115 NE2 = 2.30 Å · Zn ⋯ Asp126 OD2 = 1.93 Å · Zn ⋯ Glu52 OE1 = 1.96 Å · Ser123 OG ⋯ Zn = 4.10 Å · Ser123 OG ⋯ Asp126 OD2 = 3.56 Å S2 — Sequence/annotation: UniProt O00487 (human PSMD14 / POH1) · NCBI Gene 10213 — JAMM Zn-binding His113 / His115 / Asp126 S3 — 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, the water docked at Zn / its hydroxide, product release), the pose is drawn schematically and labeled as such in the narration.

PSMD14 JAMMZn²⁺ONH⁺ (gold)nucleophile (blue)