Ribose-5-phosphate isomerase - 3D Mechanism Simulator

Loading structural data… (1O8B)

References & Databases

START HERE — how to read Ru5P ⇌ R5P A single aldose–ketose isomerization cartoon on a bacterial RpiA pocket. Real crystal: 1O8B (1.25 Å) E. coli RpiA with deposited arabinose-5-P (ABF), a cyclic analog. Human RPIA (P49247) has no PDB — this mesh is a species hedge. Ru5P and R5P are [schematic] open-chain poses on the analog seat. Glu103 ★ and Asp81 ★ invert C1/C2 via a cis-enediolate. Measured Å are analog contacts on 1O8B only. Net: Ru5P ⇌ R5P — no net H⁺. This is not RPE (that enzyme makes Xu5P). R5P feeds TKT and nucleotides.
Crystal structure PDB 1O8B — E. coli ribose-5-phosphate isomerase A + arabinose-5-P, 1.25 Å (Zhang et al. 2003, PMID 12517338). Coordinates are public. Mesh = chain B, residues 2–218 (Cα gaps at disordered loops; MSE → MET). Related apo: 1LKZ. Human RPIA UniProt P49247 has no PDB. NCBI Gene 22934.
Mechanism — two-face acids, cis-enediolate, C1/C2 isomerize EC 5.3.1.6 isomerizes D-ribulose 5-phosphate to D-ribose 5-phosphate (Rhea 13621). This page: Glu103 ★ / Asp81 ★ invert C1/C2 through a cis-enediolate; Ru5P fades in place to R5P. Compiled RPI writes abstraction and reprotonation as one event; the screen shows the stereochemical outcome as one beat. ABF atom names: O2 faces Glu103, O1 faces Asp81, phosphate O3X faces Ser30. Source: UniProt P0A7Z0 (E. coli) · human P49247 · Rhea 13621 · PDB 1O8B · PMID 12517338
0 — Setup: analog occupancy, empty catalytic story The pocket presents deposited ABF (cyclic analog) as occupancy, not the open-chain substrate. Opaque, run:null (no autoplay). Human P49247 has no PDB; this mesh is E. coli. Glu103 ★ / Asp81 ★ are the two-face pair.Source: PDB 1O8B (1.25 Å)
① — Ru5P binds (open-chain schematic) [schematic] Open-chain Ru5P is seated on the ABF analog pocket. ABF is cyclic; the catalytic substrate is linear. Not a deposited ternary.Source: schematic pose on 1O8B ABF seat
② — Two-face acids (analog Glu103⋯O2) Deposited analog: Glu103 OE1 ⋯ ABF O2 = 2.61 Å on 1O8B. That Å is the cyclic analog, not open-chain Ru5P. Asp81 OD1 ⋯ ABF O1 = 2.96 Å is the other analog contact. Overlay/schematic sugar Å are not geomClaims.Source: 1O8B ABF-B + Glu103 / Asp81
③ — C1/C2 isomerize: Ru5P → R5P (hypothetical, lit.-based) Glu103 ★ and Asp81 ★ invert C1/C2 through a cis-enediolate [schematic]. Ru5P cross-fades in place to R5P. Compiled RPI writes this as one event; the screen shows the stereochemical outcome as one beat. Slow-motion on purpose.Source: compiled EC 5.3.1.6 · Zhang 2003
④ — R5P leaves [schematic] R5P departs. Net Ru5P ⇌ R5P — no net H⁺. R5P feeds nucleotide synthesis and TKT. This is not RPE (Xu5P).Source: PPP bookkeeping · EC 5.3.1.6

How to read this page — a first-pass primer First pass: Setup (ABF analog occupancy) → ① Ru5P docks (open-chain schematic) → ② analog Glu103⋯O2 measured → ③ C1/C2 isomerize, Ru5P becomes R5P → ④ R5P leaves. Second pass: only analog Å are printed — open-chain poses are schematic. Third pass: open “Disagreements” for analog vs substrate, species hedge, and concerted vs one-beat.
Chemistry primer — aldose–ketose isomerization Ru5P is a ketose (carbonyl at C2); R5P is an aldose (carbonyl at C1). Two acids take and return a proton on opposite faces through a cis-enediolate. Net: Ru5P ⇌ R5P. No NADP, no net H⁺. RPE makes Xu5P instead.
Words used on screen — analog · two-face · schematic Analog — ABF is cyclic arabinose-5-P trapped in 1O8B, not open-chain Ru5P. Two-face — Glu103 ★ and Asp81 ★ work from opposite faces of C1/C2. Schematic — Ru5P/R5P are open-chain teaching poses on the analog seat, not a deposited ternary.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 1O8B (1.25 Å) E. coli RpiA with ABF analog and Glu103 / Asp81 / Ser30 / Lys121. The inferred layer (all [schematic]): open-chain Ru5P, R5P, cis-enediolate, and product leave. Analog Å are geomClaims. Schematic sugar contacts are not. Binding order is compiled staging, not a kinetic fit. The protein mesh is static.
Disagreements on record (a) Analog vs substrate. 1O8B holds cyclic ABF, not open-chain Ru5P. Open-chain poses are schematic; analog Å are not substrate claims. (b) Concerted vs one-beat. Compiled RPI writes C1/C2 abstraction + reprotonation as one event; this page shows the stereochemical outcome as one beat (③). (c) Species. Human P49247 has no PDB — this mesh is E. coli (P0A7Z0). Residue numbers are 1O8B. (d) Cα gaps. Chain B 2–218 has disordered loops (212 Cα including MSE); gaps are crystal, not a truncated gene. (e) RPE vs RPI. RPI makes R5P; RPE makes Xu5P.
Regulation — non-oxidative PPP · isoforms RPI sits after PGD on non-oxidative PPP and splits Ru5P toward R5P (this page) while RPE makes Xu5P. Human RPIA (P49247) is the gene named; the mesh is bacterial. No allosteric crystal is claimed here.Source: UniProt P49247 · textbook PGD → RPI / RPE
Kinetics scope (no measured timecourse on this page) One Ru5P ⇌ R5P event is drawn, not a steady-state run. Compiled BRENDA values for EC 5.3.1.6 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 5.3.1.6 — no k_cat/K_m re-asserted
Sequence Human RPIA UniProt P49247 · NCBI Gene 22934. Residue numbers on this screen are 1O8B E. coli (Glu103, Asp81, Ser30, Lys121).
Simulation map — what you see is what is written Setup = 1O8B pocket with ABF analog occupancy (opaque, run:null). ① Ru5P moves in (open-chain schematic). ② analog Glu103⋯O2 2.61 Å after dock. ③ slow-mo: Glu103 ★ / Asp81 ★ invert C1/C2; Ru5P fades to R5P. ④ R5P leaves. Only these events move.
Sources — bibliography of this page S1 — PDB 1O8B: E. coli RpiA + ABF, 1.25 Å — public coordinates (Zhang 2003, PMID 12517338) S2 — Sequence: UniProt P0A7Z0 (E. coli) · human P49247 · NCBI Gene 22934 · Rhea 13621 S3 — Related apo: PDB 1LKZ S4 — Kinetics: BRENDA EC 5.3.1.6 — no k_cat/K_m re-asserted on this page

› Backbones and analog occupancy are taken directly from the listed PDB entry. 1O8B holds cyclic ABF, not open-chain Ru5P. Where no crystalline state exists on this frame (open-chain Ru5P, R5P, cis-enediolate, product release), the pose is drawn schematically and labeled as such in the narration.

N-domainC-domainON