Ribulose-5-phosphate 3-epimerase - 3D Mechanism Simulator

Loading structural data… (3OVP)

References & Databases

START HERE — how to read Ru5P ⇌ Xu5P A single C3-epimerization cartoon on a human RPE pocket. Real crystal: 3OVP (1.70 Å) human hRPE with deposited Fe²⁺ (residue 229). No sugar is in 3OVP; Ru5P is a 3OVQ overlay and Xu5P a 3OVR overlay — both [schematic]. Fe²⁺ is a Lewis acid (His35 / Asp37 / His70 / Asp175), not a redox cofactor. Asp37 ★ and Asp175 ★ invert C3 via a cis-enediolate. Measured Å are Fe–ligand pairs on 3OVP only. Overlay sugar⋯Fe contacts are teaching geometry, not geomClaims. XPE (PEG) is crystallization buffer, not extracted. Net: Ru5P ⇌ Xu5P — no net H⁺. Xu5P feeds TKT.
Crystal structure PDB 3OVP — human ribulose-5-phosphate 3-epimerase, 1.70 Å, with Fe²⁺ A229. Coordinates are public. Chain A, residues 4–224 (Cα gaps at disordered loops). HET = FE2 229, XPE (PEG buffer — not extracted), HOH. Sugar co-crystals: 3OVQ (2.00 Å, 5RP = Ru5P) and 3OVR (1.95 Å, 5SP = Xu5P) are overlaid by Cα Kabsch onto 3OVP-A. Human RPE UniProt Q96AT9 · NCBI Gene 6120.
Mechanism — Fe²⁺ Lewis acid, two-face Asp, C3 invert EC 5.1.3.1 epimerizes D-ribulose 5-phosphate at C3 to D-xylulose 5-phosphate (Rhea 13625). This page: Fe²⁺ polarizes the C2 carbonyl; Asp37 ★ / Asp175 ★ invert C3 through a cis-enediolate; Ru5P fades in place to Xu5P. Compiled RPE writes abstraction and reprotonation as one event; the screen shows the stereochemical outcome as one beat. Deposited 5RP/5SP names: C3 = carbonyl C2, O4 = carbonyl O2, C5 = epimeric C3, O13 = C3-OH. Source: UniProt Q96AT9 · Rhea 13625 · PDB 3OVP · 3OVQ · 3OVR
0 — Setup: Fe²⁺ pocket, no sugar The catalytic TIM-barrel presents deposited Fe²⁺ (residue 229). 3OVP has no sugar — XPE is PEG buffer — so the pocket is shown with Fe only. Opaque, run:null (no autoplay). Asp37 ★ / Asp175 ★ are the two-face pair; His35 / His70 complete the Fe shell.Source: PDB 3OVP (1.70 Å)
① — Ru5P binds (3OVQ overlay) [schematic] Ru5P is seated from 3OVQ 5RP onto this 3OVP mesh. Carbonyl O2 = O4, epimeric C3 = C5, C3-OH = O13. Overlay O4/O13⋯Fe contacts are teaching geometry, not geomClaims. Not a deposited ternary.Source: 3OVQ overlay onto 3OVP (Cα Kabsch)
② — Fe²⁺ polarizes the C2 carbonyl Deposited Fe²⁺ is a Lewis acid. His35 NE2 ⋯ FE = 2.18 Å is measured on 3OVP. Overlay sugar⋯Fe distances are not geomClaims. Fe does not change oxidation state.Source: 3OVP FE2 A229 + His35 / Asp37 / His70 / Asp175
③ — C3 inverts: Ru5P → Xu5P (hypothetical, lit.-based) Asp37 ★ and Asp175 ★ invert epimeric C3 (deposited name C5) through a cis-enediolate [schematic]. Ru5P cross-fades in place to Xu5P (3OVR overlay). Compiled RPE writes this as one event; the screen shows the stereochemical outcome as one beat. Slow-motion on purpose.Source: compiled EC 5.1.3.1 · 3OVR overlay
④ — Xu5P leaves — Fe²⁺ stays [schematic] Xu5P departs. Deposited Fe²⁺ stays. Net Ru5P ⇌ Xu5P — no net H⁺. Xu5P is a ketol donor for TKT.Source: PPP bookkeeping · EC 5.1.3.1

How to read this page — a first-pass primer First pass: Setup (Fe²⁺ pocket, no sugar) → ① Ru5P docks (3OVQ overlay) → ② Fe polarizes C2 (measured His35⋯FE) → ③ C3 inverts, Ru5P becomes Xu5P → ④ Xu5P leaves, Fe stays. Second pass: only Fe–ligand Å are printed — sugar poses are overlays. Third pass: open “Disagreements” for overlay vs ternary, two-face Asp, and concerted vs one-beat.
Chemistry primer — C3 epimerization Ru5P and Xu5P differ only at C3. Fe²⁺ polarizes the C2 ketone; two aspartates take and return a proton on opposite faces of C3 through a cis-enediolate. Net: Ru5P ⇌ Xu5P. No NADP, no net H⁺. TKT uses Xu5P next.
Words used on screen — Lewis acid · two-face · overlay Lewis acid — Fe²⁺ polarizes the carbonyl; it is not a redox cofactor here. Two-face — Asp37 ★ and Asp175 ★ work from opposite faces of C3. Overlay — Ru5P/Xu5P coordinates come from 3OVQ/3OVR, seated onto 3OVP by Cα Kabsch; not a deposited ternary. 5RP/5SP names — C3=C2 carbonyl carbon, O4=O2, C5=epimeric C3, O13=C3-OH.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 3OVP (1.70 Å) human RPE with Fe²⁺ A229 and His35 / Asp37 / His70 / Asp175. Deposited XPE is PEG buffer, not drawn as sugar. The inferred layer (all [schematic]): Ru5P (3OVQ overlay), Xu5P (3OVR overlay), cis-enediolate, and product leave. Fe–ligand Å are geomClaims. Overlay sugar⋯Fe contacts are not. Binding order is compiled staging, not a kinetic fit. The protein mesh is static.
Disagreements on record (a) Overlay vs ternary. 3OVP has Fe, not sugar. 3OVQ/3OVR sugars are Kabsch-seated [schematic]; overlay Å are not geomClaims. (b) Concerted vs one-beat. Compiled RPE writes C3 abstraction + reprotonation as one event; this page shows the stereochemical outcome as one beat (③). (c) Metal identity. 3OVP deposits Fe²⁺; some RPE orthologs use Zn²⁺ or Mn²⁺ — this page draws the deposited iron. (d) Cα gaps. Chain A 4–224 has disordered loops (205 Cα); gaps are crystal, not a truncated gene. (e) XPE. PEG buffer, not substrate.
Regulation — non-oxidative PPP · isoforms RPE sits after PGD on non-oxidative PPP and feeds Xu5P to TKT. Cytosolic RPE (this page, Q96AT9) is the human gene drawn. No allosteric crystal is claimed here.Source: UniProt Q96AT9 · textbook PGD → RPE → TKT
Kinetics scope (no measured timecourse on this page) One Ru5P ⇌ Xu5P event is drawn, not a steady-state run. Compiled BRENDA values for EC 5.1.3.1 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 5.1.3.1 — no k_cat/K_m re-asserted
Sequence Human RPE UniProt Q96AT9 · NCBI Gene 6120. Residue numbers on this screen are 3OVP (His35, Asp37, His70, Asp175, Fe A229).
Simulation map — what you see is what is written Setup = 3OVP catalytic pocket with Fe²⁺ only (opaque, run:null). ① Ru5P moves in (3OVQ overlay). ② Fe polarizes C2; His35⋯FE 2.18 Å after dock. ③ slow-mo: Asp37 ★ / Asp175 ★ invert C3; Ru5P fades to Xu5P. ④ Xu5P leaves; Fe stays. Only these events move.
Sources — bibliography of this page S1 — PDB 3OVP: human RPE, 1.70 Å, Fe²⁺ A229 — public coordinates; XPE = PEG buffer S2 — Sugar overlays: PDB 3OVQ (5RP / Ru5P) · PDB 3OVR (5SP / Xu5P) S3 — Sequence: UniProt Q96AT9 · NCBI Gene 6120 · Rhea 13625 S4 — Kinetics: BRENDA EC 5.1.3.1 — no k_cat/K_m re-asserted on this page

› Backbones are taken directly from the listed PDB entry. 3OVP holds Fe²⁺, not a sugar. Where no crystalline state exists on this frame (Ru5P, Xu5P, cis-enediolate, product release), the pose is drawn schematically and labeled as such in the narration.

N-domainC-domainONFe²⁺