UBA1 - 3D Mechanism Simulator

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References & Databases

START HERE — how to read Ub + ATP → E1~Ub + AMP + PPi A two-half-reaction E1 cartoon on the human UBA1 frame that actually exists: 6DC6 (3.14 Å) with crystal ubiquitin + POP (PPi) + Mg×2. Occupancy is Ub·POP·Mg, not ATP and not E1~Ub thioester. Residue 632 is ALA (C632A) — compiled Cys632 thiol. Ala632 CB stands ~34.5 Å from Gly76 C on this snapshot. ATP, AMP, Ub-AMP analog, and the thioester are [schematic] in pose — but the ATP molecular geometry (ring closure, bond lengths/angles) is the real experimental conformer from 4II2 (S. pombe Uba1 + ubiquitin + ATP/Mg, 2.20 Å, ATP A1103), its β/γ phosphates Kabsch-fit to the crystal POP (RMSD 0.30 Å); AMP and Ub-AMP are built from that ATP. The pose stays [schematic] because 6DC6 holds PPi, not ATP, and 4II2 is a different species' E1. Ala632 ★ is the compiled E1 thiol analog. White is nucleotidyl P-attack (Gly-OXT → ATP PA). Blue is the Cys-S nucleophile that glides in and seats as the C-domain closes, then attacks the carbonyl at the active site (the raw residue-632 CB is far), not hydride. Measured Å are deposited 6DC6 pairs only. E2 transfer is not this page. Gap 804–820 is named. Chains C/D are a copy, not this mesh. 4P22 is an N-terminal fragment, not this fold. Not a pure A-page (covalent E~Ub).
Crystal structures PDB 6DC6 — human UBA1 (UNP 49–1058) + ubiquitin + POP + MG, 3.14 Å (Lv 2018). Coordinates are public. Residue 632 is ALA (SEQADV C632A). 4P22 is an N-terminal fragment — not this mesh. UniProt P22314. The substrate ATP is not modeled on 6DC6; its molecular geometry is taken from PDB 4II2 — S. pombe Uba1 with ubiquitin + ATP/Mg (2.20 Å, ATP A1103) — superposed onto the 6DC6 POP by a β/γ-phosphate Kabsch fit (RMSD 0.30 Å), so only its pose stays [schematic] (4II2 is a different species' E1).
Mechanism — two E1 half-reactions UBA1 is the ubiquitin E1: ubiquitin + ATP → E1~Ub thioester + AMP + PPi (EC 6.2.1.45). (1) Ub C-terminus attacks ATP α-P → Ub-AMP + PPi. (2) Cys632-SH attacks that carbonyl → E1~Ub + AMP. Lv et al., J. Biol. Chem. 2018, PMID:30279270. E2/E3 cascade is not this path. Source: Lv 2018 · UniProt P22314 · ubiquitin P62979
0 — Setup: Mg present, pocket shown empty 6DC6 holds Ub Gly76 + POP + Mg×2. The pocket is shown empty so ordered binding can start. Both Mg stay as named occupants. Opaque, run:null (no autoplay). Residue 632 is ALA (C632A). Ala632 ★ is the compiled E1 thiol analog.Source: PDB 6DC6 (3.14 Å)
① — Ubiquitin C-terminus binds Crystal ubiquitin Gly76 docks as the C-terminus — real 6DC6 occupancy. Carboxylate faces the nucleotide / Mg / POP seat. Gly76 is the ligand, not on the ubiquitin tube. This is not ATP and not the thioester.Source: 6DC6 ubiquitin chain B Gly76
② — ATP binds [schematic ATP pose] docks onto the crystal POP (PPi) seat — 6DC6 holds PPi, not ATP. The ATP molecular geometry is the real 4II2 ATP A1103 conformer, β/γ-fit to POP. Gly76 C ⋯ POP O4 = 4.90 Å. Mg ⋯ POP O6 = 2.19 Å. This is not AMP and not the thioester. Residue 632 is still ALA; Ala632 CB still stands ~34.5 Å from Gly76 C.Source: 6DC6 POP-A1103 / MG-A1101; ATP geometry from 4II2 A1103 (pose schematic)
③ — Gly-OXT attacks ATP α-P → Ub-AMP + PPi (hypothetical, lit.-based) White phosphoryl rides from Ub C-terminal OXT to schematic ATP PA. Gly76 + ATP fade in place to schematic Ub-AMP analog and crystal PPi (POP). This is not deposited mixed anhydride — 6DC6 holds free Gly76 + POP. Residue 632 is not yet the nucleophile. Slow-motion on purpose. White = nucleotidyl P-attack, not hydride.Source: compiled E1 adenylation · Lv 2018
④ — PPi leaves Crystal PPi (POP) departs. The Ub-AMP analog stays as teaching occupancy. Asp576 OD2 ⋯ Mg = 2.17 Å is the deposited metal ligand. Ala632 CB still stands ~34.5 Å from Gly76 C on this crystal — the next attack is [schematic], not this snapshot.Source: 6DC6 Asp576 / MG; crystal POP
⑤ — Cys632-S attacks carbonyl → E1~Ub + AMP (hypothetical, lit.-based) Blue nucleophile (compiled Cys632-S) glides in from inside the cleft, seats beside the Ub-AMP analog carbonyl, then a short blue arrow runs S → carbon at the active site — drawn as if the C-domain has closed and brought the thiol in. Ub-AMP fades in place to schematic E1~Ub thioester (Gly76 carbonyl now bonded to Cys632-S) and schematic AMP at the nucleotide seat. On this C632A crystal the residue-632 CB stands ~34.5 Å from Gly76 C, so the approach pose and thioester geometry are [schematic], not deposited. Second E1 half-reaction. Not a pure A-page. Slow-motion on purpose. Blue = sulfur nucleophile, not hydride.Source: compiled E1 thioesterification · UniProt P22314 Cys632
⑥ — AMP leaves — E2 not this page [schematic AMP] AMP departs. Schematic E1~Ub thioester stays on compiled Cys632. Both Mg stay. PPi already left with the first half-reaction. E2 transfer is not this page.Source: ubiquitin E1 bookkeeping · Lv 2018

How to read this page — a first-pass primer First pass: Setup (Mg present, pocket empty, Ala632 ★, C632A) → ① Gly76 docks → ② ATP (real 4II2 molecular geometry, schematic pose) docks on POP seat → ③ white Gly-OXT → ATP PA, fade to Ub-AMP analog + PPi → ④ PPi leaves → ⑤ blue compiled Cys632-S glides in and seats beside the carbonyl, then short arrow → carbonyl, fade in place to E1~Ub + AMP → ⑥ AMP leaves; thioester stays; E2 not this page. Second pass: 4.90 / 2.19 / 2.17 Å are crystal facts on 6DC6; the ATP molecular geometry is real (4II2 A1103, β/γ-fit to POP), while its pose, AMP, Ub-AMP, and the thioester are [schematic]. White = nucleotidyl P-attack. Blue = Cys-S. Third pass: open “Disagreements” for C632A, POP ≠ ATP, occupancy ≠ thioester, Ala632 ~34.5 Å, and E2 not this path.
Chemistry primer — E1 adenylation then thioester UBA1 activates ubiquitin in two half-reactions. The C-terminal carboxylate attacks ATP α-P; PPi leaves and a Ub-AMP mixed anhydride forms. Cys632-SH then attacks that carbonyl; AMP leaves and the product is E1~Ub thioester, the substrate of an E2. Gold is unused on this page (no catalytic H⁺ sphere). White = nucleotidyl P-attack (Gly-OXT → ATP PA). Blue = sulfur nucleophile that glides in and seats, then attacks the carbonyl at the active site, not hydride. This is not E2 transfer and not the proteasome.
Words used on screen — C632A · POP ≠ ATP · E1 C632A — residue 632 on 6DC6 is ALA (SEQADV); compiled Cys632 is the E1 thiol. POP ≠ ATP — deposited ligand is pyrophosphate, not ATP. E1 — ubiquitin-activating enzyme (two half-reactions). Product-like occupancy — deposited Ub + free Gly76 + POP, not intact Ub-AMP and not E1~Ub.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 6DC6 (3.14 Å) human UBA1 with ubiquitin, POP, MG×2; Asp576 OD2 ⋯ MG = 2.17 Å; Asp506 OD2 ⋯ MG2 = 2.00 Å; Glu509 OE2 ⋯ MG2 = 2.79 Å; MG ⋯ POP O6 = 2.19 Å; MG ⋯ POP O2 = 2.86 Å; MG2 ⋯ POP O5 = 2.60 Å; Arg57 NH1 ⋯ POP P1 = 3.54 Å; Lys528 NZ ⋯ POP P2 = 3.70 Å; Gly76 C ⋯ POP O4 = 4.90 Å. The inferred layer ([schematic]): the ATP pose (its molecular geometry is real, transplanted from 4II2 ATP A1103), Ub-AMP analog, AMP, E1~Ub thioester (drawn at the active site — Cys632 has to swing in; the raw residue-632 CB is far), transferring nucleophile spheres, product leave. Ala632 CB ⋯ Gly76 C ≈ 34.5 Å is deposited and is not a close-attack claim. It is the open (adenylation) snapshot, not the attack path — in real catalysis the flexibly linked Cys-domain (cross-over loop) swings in to the active site, so a flying arrow from the far residue would be biology-wrong; the compiled local swing-in + short arrow drawn here is the real picture. Binding order is compiled staging, not a kinetic fit. The protein mesh is static.
Disagreements on record (a) C632A ≠ WT Cys632. Residue 632 is ALA; compiled Cys632 thiol. (b) POP ≠ ATP. Crystal holds PPi, not ATP. (c) Occupancy ≠ thioester. Crystal holds free Gly76 + POP, not E1~Ub and not intact Ub-AMP. (d) Ala632 is far. CB ⋯ Gly76 C ≈ 34.5 Å on this snapshot; thioester geometry is schematic. (e) Concerted vs split. Compiled E1 writes two half-reactions; this page splits them (③ then ⑤) for 1-event/1-step teaching. (f) E2/E3 cascade is not this path. (g) 4P22 N-terminal fragment is not this mesh. (h) Chains C/D are a copy, not this mesh. (i) Gap 804–820 is missing. (j) Ubiquitin on this deposit is UniProt P62979 (RS27A). (k) ATP geometry source. 6DC6 models no ATP; the real ATP molecular geometry is transplanted from 4II2 (S. pombe Uba1 + ATP/Mg — not human), so the molecule is experimental but its pose is [schematic].
Regulation — E2 cascade named, not shown This mesh is human UBA1 activating ubiquitin. Transfer to E2 (and later E3) is hub-false on this path — named, not motion. Proteasome cutting is a later id (PSMB5). NEDD8 / SUMO E1 enzymes are other genes.Source: UniProt P22314 · Lv 2018
Kinetics scope (no measured timecourse on this page) One ubiquitin + ATP → E1~Ub + AMP + PPi event is drawn, not a steady-state run. No measured k_cat/K_m is re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: Lv 2018 — no k_cat/K_m re-asserted
Sequence Human UBA1 UniProt P22314 · ubiquitin P62979 · NCBI Gene 7317. This screen uses human numbering (Ala632 on 6DC6 = UniProt Cys632). Chain A Cα 49–1057, gap 804–820. Ubiquitin chain B Cα 1–75 offset +1000. Gly76 is the ligand, not on the tube.
Simulation map — what you see is what is written Setup = 6DC6 pocket empty, both Mg visible (opaque, no autoplay). ① crystal Gly76 moves in. ② schematic ATP moves in. ③ slow-mo: white Gly-OXT → ATP PA; Gly76+ATP fade to Ub-AMP analog + PPi. ④ crystal PPi leaves. ⑤ slow-mo: blue compiled Cys632-S glides in, seats, then short arrow → carbonyl; analog fades in place to E1~Ub + AMP. ⑥ AMP leaves; thioester stays; E2 not this page. Only these events move.
Sources — bibliography of this page S1 — PDB 6DC6: human UBA1·Ub·POP·Mg, 3.14 Å — public coordinates; measured C⋯O4 = 4.90 Å · O6⋯Mg = 2.19 Å · OD2⋯Mg = 2.17 Å S2 — Lv et al., J. Biol. Chem. 2018, PMID:30279270 — human UBA1–ubiquitin complex; conserved E1 elements S3 — Sequence: UniProt P22314 (UBA1) · P62979 (ubiquitin) · NCBI Gene 7317 S4 — Kinetics: no k_cat/K_m re-asserted on this page S5 — PDB 4II2: S. pombe Uba1 + ubiquitin + ATP/Mg, 2.20 Å — the real ATP A1103 conformer transplanted onto the 6DC6 POP by a β/γ-phosphate Kabsch fit (RMSD 0.30 Å); the pose stays [schematic] (a different species' E1)

› 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., ATP, Ub-AMP, AMP, E1~Ub thioester, nucleophile flight, product release), the pose is drawn schematically and labeled as such in the narration.

UBA1ubiquitinONphosphoryl (white)nucleophile (blue)