PSMB5 - 3D Mechanism Simulator

Loading structural data… (5LE5)

References & Databases

START HERE — how to read peptide + H₂O → fragments on proteasome β5 A single chymotrypsin-like cut cartoon on the native human 20S β5 frame that exists: 5LE5 (1.80 Å), chain K, with an empty mature cleft. That occupancy is not a peptide and not bortezomib. PDB Thr1 is UniProt Thr60 (propeptide off). The hydrophobic analog, N-fragment, C-fragment, and water are [schematic]. Thr1 ★ is the N-terminal nucleophile. Blue is Thr1-OG1 nucleophile, not a hydride. Gold H⁺ leaves water. Measured Å are deposited 5LE5 protein pairs only. Overlay peptide distances are not geomClaims. Chain Y is a copy, not this mesh. β1/β2 are other catalytic subunits, named not shown. 5LF3 bortezomib soaks are a named overlay, not this mesh. Gap 202–204 is missing. 20S is named context; teaching = β5 Thr1. Not a pure A-page (E~acyl covalent).
Crystal structures PDB 5LE5 — native human 20S proteasome, 1.80 Å (Schrader 2016). Coordinates are public. Chain K = PSMB5 UniProt P28074 60–263 (PDB 1–204). 5LF3 bortezomib soaks are a named overlay — not this mesh. UniProt P28074.
Mechanism — Thr1 N-terminal nucleophile, ester, water hydrolysis PSMB5 is 20S β5: peptide + H₂O → N-fragment + C-fragment (EC 3.4.25.1, chymotrypsin-like). Thr1 OG1 attacks the scissile carbonyl; a covalent ester forms; water then hydrolyses E~acyl. Schrader et al., Science 2016, PMID:27493187. UniProt P28074 nucleophile is Thr60 = PDB Thr1. Product teaching = cleaved hydrophobic-Xaa peptide. Physiological proteasome substrates are analog, not this mesh. Source: Schrader 2016 · UniProt P28074
0 — Setup: empty mature β5 cleft 5LE5 holds mature β5 with an empty cleft. That occupancy is not a peptide and not bortezomib. Opaque, no autoplay. Chemistry below uses a schematic hydrophobic analog. PDB Thr1 = UniProt Thr60.Source: PDB 5LE5
① — hydrophobic analog presented A short hydrophobic analog docks as a named stand-in for a chymotrypsin-like cut — [schematic], not a peptide crystal and not bortezomib. Carbonyl faces Thr1 OG1. Overlay peptide Å are not geomClaims.Source: compiled β5 substrate identity · UniProt P28074
② — Thr1 attacks C → covalent E~acyl (hypothetical, lit.-based) Blue nucleophile rides from Thr1 OG1 to analog C. Intact peptide fades in place to schematic N-fragment + C-fragment (ester). Overlay peptide Å are not geomClaims. Slow-motion on purpose. Not a pure A-page.Source: compiled Ntn hydrolase · UniProt P28074
③ — C-fragment leaves (hypothetical, lit.-based) Schematic C-fragment departs. E~acyl stays on Thr1 OG1. Cut teaching = hydrophobic-Xaa opened at one site.Source: EC 3.4.25.1 net accounting
④ — Water hydrolyses E~acyl (hypothetical, lit.-based) A schematic water glides up to the ester carbonyl. A gold H⁺ leaves water H2 on the yellow arrow and vanishes right at the arrow tip; the remaining OH⁻ attacks the ester carbon and its O becomes the N-fragment carboxylate oxygen, riding out bound to the product (red ball). The ester is hydrolysed. Water is consumed. Overlay hydrolysis Å are not geomClaims.Source: compiled Ntn hydrolase hydrolysis · UniProt P28074
⑤ — N-fragment leaves — cut [schematic] N-fragment departs. Product teaching = cleaved hydrophobic-Xaa peptide. The empty cleft was occupancy, not this chemistry. β1/β2 are other catalytic subunits, named not shown. 5LF3 bortezomib is not this mesh.Source: EC 3.4.25.1 net accounting

How to read this page — a first-pass primer First pass: Setup (empty mature cleft, Thr1 ★) → ① hydrophobic analog docks → ② blue OG1 → C, peptide becomes N + C fragments → ③ C-fragment leaves → ④ gold H⁺ then OH⁻ attacks E~acyl → ⑤ N-fragment leaves; cut. Second pass: 2.72 / 2.98 / 2.75 / 2.81 / 3.28 Å are crystal facts on empty-cleft 5LE5 atoms; peptide, fragments, water, and H spheres are [schematic]. Third pass: open “Disagreements” for empty ≠ peptide, Thr1 = UniProt Thr60, 5LF3 not this mesh, and β1/β2 as other subunits.
Chemistry primer — N-terminal nucleophile hydrolase, chymotrypsin-like β5 cuts after hydrophobic residues via a threonyl ester, then water hydrolyses E~acyl. Gold = H⁺. Blue = Thr1-OG1 nucleophile (not hydride). Teaching substrate = hydrophobic analog. This is not β1 (caspase-like) and not β2 (trypsin-like). This is not bortezomib occupancy.
Words used on screen — occupancy · analog · Ntn · empty cleft Occupancy — the empty mature β5 cleft is the crystal; never relabeled as peptide or bortezomib. Analog — the peptide is a short model occupancy for a chymotrypsin-like cut. Ntn — N-terminal nucleophile (Thr1). Empty cleft — no peptide and no bortezomib on chain K.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 5LE5 (1.80 Å) native human 20S β5 chain K empty cleft; Thr1 OG1 ⋯ Lys33 NZ = 2.72 Å; Thr1 N ⋯ Ser130 OG = 2.98 Å; Thr1 N ⋯ Tyr169 O = 2.75 Å; Lys33 NZ ⋯ Asp17 OD1 = 2.81 Å; Thr1 N ⋯ Ser170 OG = 3.28 Å. The inferred layer ([schematic]): hydrophobic analog, N/C fragments, E~acyl, 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 peptide contacts are not geomClaims. Residue 169 is TYR.
Disagreements on record (a) Empty cleft ≠ peptide ≠ bortezomib. Occupancy. (b) PDB Thr1 = UniProt Thr60. Propeptide is off. (c) Peptide ≠ physiological proteasome substrate. Hydrophobic analog is a model occupancy. (d) Capture vs hydrolysis split. Compiled Ntn hydrolase writes two chemical events; this page plays five beats. (e) β1/β2 are other catalytic subunits, named not shown. (f) 5LF3 bortezomib is not this mesh. (g) Chain Y is a copy, not this mesh. (h) Gap 202–204 is missing. (i) No protein-domain swing. (j) Not a pure A-page — E~acyl is covalent. (k) 20S is named context — teaching mesh is β5 chain K, not 28-chain spaghetti. (l) Residue 169 is TYR, not Gly.
Regulation — 20S · immunoproteasome · inhibitors 20S assembly is named context, not a morph. Immunoproteasome β5i (PSMB8) is another gene, not this page. Bortezomib is a compiled inhibitor (5LF3), not this mesh.Source: UniProt P28074 · Schrader 2016 PMID:27493187
Kinetics scope (no measured timecourse on this page) One hydrophobic-Xaa cleavage event is drawn, not a steady-state run. Compiled BRENDA values for EC 3.4.25.1 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 3.4.25.1 — no k_cat/K_m re-asserted
Sequence Human PSMB5 UniProt P28074 · NCBI Gene 5693. Screen uses 5LE5 numbering. PDB Thr1 = UniProt Thr60. Residue 169 is TYR.
Simulation map — what you see is what is written Setup = 5LE5 empty mature cleft (opaque, no autoplay). ① hydrophobic analog moves in (schematic). ② slow-mo: blue nucleophile OG1 → C; peptide fades to N + C fragments. ③ C-fragment leaves. ④ gold H⁺ then OH⁻ attacks E~acyl. ⑤ N-fragment leaves; cut. Only these events move.
Sources — bibliography of this page S1 — PDB 5LE5: native human 20S proteasome, 1.80 Å — public coordinates; measured OG1⋯NZ = 2.72 Å · N⋯Ser130 OG = 2.98 Å · N⋯Tyr169 O = 2.75 Å · NZ⋯Asp17 OD1 = 2.81 Å · N⋯Ser170 OG = 3.28 Å S2 — Schrader et al., Science 2016, PMID:27493187 — native human 20S at 1.8 Å S3 — Sequence: UniProt P28074 (human PSMB5) · NCBI Gene 5693 S4 — Kinetics: BRENDA EC 3.4.25.1 — no k_cat/K_m re-asserted on this page

› 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., hydrophobic analog, N/C fragments, ester, H⁺ flight, product release), the pose is drawn schematically and labeled as such in the narration.

β5 N-barrelβ5 C-barrelONH⁺ (gold)nucleophile (blue)