PLCδ1 - 3D Mechanism Simulator

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References & Databases

START HERE — how to read PIP₂ + H₂O → IP₃ + DAG on PLCδ1 One hydrolysis cartoon on rat phospholipase C-δ1 (PLCδ1): 1DJX (2.30 Å) = PLCδ1 (UniProt P10688), a catalytically active deletion variant lacking the N-terminal PH domain, chain A modeled author residues 200–756. The deposited occupancy is the product I3P = IP₃ (D-myo-inositol-1,4,5-trisphosphate) plus the required catalytic Ca²⁺ (A 2). A second calcium (A 3) is a C2-domain site (Ile651 O / Asp653 / Asn677) — it is context only, not the catalytic metal. The substrate PtdIns(4,5)P₂ (PIP₂) is not modeled, so it is [schematic] (the I3P pose plus a small glycerol/DAG stub esterified at the 1-phosphate P1 via the deposited O11); DAG and the catalytic hydroxide (drawn as an explicit O–H) are also [schematic]. A Ca²⁺-activated hydroxide attacks the P1 phosphate in-line; because its oxygen bonds to P1, the P1–O(DAG) bond breaks to release DAG and leave IP₃. Literature assignment: His311 putative general base, His356 putative general acid (Essen et al., Nature 1996 (structure); Biochemistry 1997 (mechanism)); Ca²⁺ ligands Asn312 / Glu341 / Asp343 / Glu390; phosphate anchors Arg549 / Lys438 / Ser522. The catalytic Ca²⁺ is required. Measured Å are deposited 1DJX chain-A pairs only.
Crystal structure — 1DJX (rat PLCδ1 / P10688 / EC 3.1.4.11) PDB 1DJX — phosphoinositide-specific phospholipase C-δ1 from rat complexed with inositol-1,4,5-trisphosphate, 2.30 Å; coordinates are public. Chain A = PLCδ1 (UniProt P10688), catalytic-domain deletion variant (PH domain absent); modeled Cα author resi 200–756 (chains A and B are copies — this page uses chain A only). Deposited ligands: I3P = IP₃ (A 1, 24 atoms), the catalytic Ca²⁺ (A 2), a C2-domain Ca²⁺ (A 3), and acetate (ACT A 5, not used). EC 3.1.4.11 (phosphoinositide phospholipase C).
Mechanism — Ca²⁺-activated hydroxide (O–H), in-line on P1, general acid/base pair PLCδ1 hydrolyses PIP₂ at the 1-phosphate: PtdIns(4,5)P₂ + H₂O → IP₃ + DAG. A Ca²⁺-activated hydroxide (drawn as an explicit O–H) is the nucleophile; its oxygen attacks P1 in-line opposite the leaving O(DAG), forms the new P–O bond, and that O becomes a phosphate oxygen of the product. The catalytic Ca²⁺ is ligated by Asn312 / Glu341 / Asp343 / Glu390 (and contacts the product phosphate) and polarises P1. Literature assigns His311 as the putative general base and His356 as the putative general acid (Essen et al., Nature 1996 (structure); Biochemistry 1997 (mechanism)); Arg549 / Lys438 / Ser522 are phosphate anchors. Source: PDB 1DJX · UniProt P10688 · BRENDA EC 3.1.4.11 · Essen et al., Nature 1996 (structure); Biochemistry 1997 (mechanism)
Setup — PLCδ1 active site (catalytic Ca²⁺) 1DJX holds the catalytic Ca²⁺ (A 2) required for turnover, ligated by Asn312 / Glu341 / Asp343 / Glu390 and contacting the product phosphate. The pocket is shown empty so binding can start; 1DJX models the product I3P, not PIP₂. Opaque, no autoplay. The chemistry below is (proposal, lit.-based). The C2-domain Ca A 3 is named as context only.Source: PDB 1DJX
① — PIP₂ docks The substrate PtdIns(4,5)P₂ docks — [schematic], not a modeled state in 1DJX (the crystal holds the product I3P). Its P1 phosphate sits on the catalytic Ca²⁺; measured register: Ca²⁺ ⋯ I3P O2 = 2.36 Å, Ca²⁺ ⋯ Glu390 OE1 = 2.28 Å, Ca²⁺ ⋯ Asn312 OD1 = 2.36 Å. Phosphate anchors: Ser522 OG ⋯ O42 = 2.58 Å, Arg549 NH1 ⋯ O3 = 2.66 Å.Source: measured 1DJX pairs · PDB 1DJX
② — Ca²⁺-activated hydroxide (O–H) attacks P1 (in-line) (hypothetical, lit.-based) A Ca²⁺-activated hydroxide (blue oxygen + its H, blue arrow) rides its oxygen in-line onto P1 opposite the leaving O(DAG), forming the new P–O bond. Drawn as an explicit O–H, not a bare O sphere. His311 is the putative general base (literature assignment); the catalytic Ca²⁺ polarises P1 and stabilises the pentacoordinate transition state (the in-line attack inverts the phosphate at P — the equatorial rig tick sweeps 180°, umbrella flip). Blue is the oxygen nucleophile, not a hydride. Slow-motion on purpose.Source: Essen et al., Nature 1996 (structure); Biochemistry 1997 (mechanism) · PDB 1DJX geometry
③ — P1–O(DAG) breaks → IP₃ + DAG (hypothetical, lit.-based) Because the hydroxide oxygen has now bonded to P1, the P1–O(DAG) bond breaks: the inositol trisphosphate is retained as the deposited IP₃ (I3P) and DAG is formed in place; the attacking O relaxes onto the vacated phosphate-O site, so it becomes a phosphate oxygen of IP₃. The pentacoordinate TBP holds through the break (rig tick at the inverted 180°). The deposited pose is this product (P1–O11 = 1.52 Å; His356 NE2 ⋯ I3P O13 = 3.06 Å). His356 is the putative general acid (literature assignment). The catalytic Ca²⁺ stays. Slow-motion on purpose.Source: product pose from PDB 1DJX · EC 3.1.4.11
④ — DAG leaves The DAG (diacylglycerol) leaving group — [schematic], built on the deposited I3P pose — departs. The deposited product IP₃ (I3P) stays and the catalytic Ca²⁺ is retained. PIP₂ hydrolysis has generated both second messengers.Source: EC 3.1.4.11 net accounting
⑤ — IP₃ leaves; site restored The product IP₃ (I3P) departs and the catalytic Ca²⁺ plus its ligands are restored, ready for the next PIP₂. Net: PtdIns(4,5)P₂ + H₂O → IP₃ + DAG (EC 3.1.4.11) — the phospholipase C step that produces IP₃ (Ca²⁺ release) and DAG (PKC activation). 1DJX modeled the product I3P; PIP₂ and DAG were schematic.Source: EC 3.1.4.11 net accounting

How to read this page — a first-pass primer First pass: Setup (empty pocket + catalytic Ca²⁺) → ① PIP₂ docks → ② blue Ca²⁺-activated hydroxide (O–H) attacks P1 in-line → ③ P1–O(DAG) breaks, PIP₂ → IP₃ + DAG → ④ DAG leaves → ⑤ IP₃ leaves, Ca²⁺ site restored. Second pass: the Å values (2.28 / 2.36 / 2.36 / 2.44 / 2.45 / 2.47 Å for Ca²⁺, and 2.58 / 2.62 / 2.66 / 2.85 / 2.88 / 2.93 / 3.06 / 3.29 / 3.48 Å for the I3P anchors) are crystal facts on 1DJX chain A atoms; PIP₂, DAG, the hydroxide (O–H) attack and the proton bookkeeping are [schematic]. Third pass: open “Disagreements” for the rat-vs-human mesh, the product-vs-substrate occupancy, and the schematic DAG/PIP₂.
Chemistry primer — phosphoinositide-specific phospholipase C PLC is a phosphodiesterase, not a kinase/phosphatase: a Ca²⁺-activated hydroxide (drawn as an explicit O–H) cuts the phosphodiester at the 1-phosphate of PIP₂. Ca²⁺ = Lewis acid that holds and polarises the phosphate. Blue = the oxygen nucleophile (not a hydride). The products are the two second messengers IP₃ and DAG. This is not a phospholipase A (acyl-chain cleavage) and not a phosphoinositide kinase (which adds the 4-/5-phosphates).
Words used on screen — occupancy · PIP₂ · I3P · in-line Occupancy — 1DJX holds the product I3P, never relabeled as PIP₂. PIP₂ — PtdIns(4,5)P₂, the substrate here (schematic pose). I3P — the PDB residue code for D-myo-inositol-1,4,5-trisphosphate, i.e. the product IP₃. In-line — the attacking hydroxide O (drawn as O–H) is placed opposite the leaving O(DAG) across P1 for an S_N2-style cut.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 1DJX (2.30 Å) chain A — Ca²⁺ ⋯ Glu390 OE1 = 2.28 Å; Ca²⁺ ⋯ Asn312 OD1 = 2.36 Å; Ca²⁺ ⋯ I3P O2 = 2.36 Å; Ca²⁺ ⋯ Asp343 OD2 = 2.44 Å; Ca²⁺ ⋯ Glu341 OE2 = 2.45 Å; Ca²⁺ ⋯ Asp343 OD1 = 2.47 Å; Ser522 OG ⋯ I3P O42 = 2.58 Å; Glu341 OE2 ⋯ I3P O3 = 2.62 Å; Arg549 NH1 ⋯ I3P O3 = 2.66 Å; Asn312 ND2 ⋯ I3P O11 = 2.85 Å; Lys438 NZ ⋯ I3P O42 = 2.88 Å; Glu390 OE1 ⋯ I3P O2 = 2.93 Å; His356 NE2 ⋯ I3P O13 = 3.06 Å; His311 NE2 ⋯ I3P O11 = 3.29 Å; Tyr551 CG ⋯ I3P C3 = 3.48 Å. The inferred layer ([schematic]): the PIP₂ substrate (I3P pose + glycerol/DAG stub), the DAG leaving group, the catalytic hydroxide (drawn as an explicit O–H), the in-line attack and the proton bookkeeping. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. The product-vs-substrate occupancy is disclosed, not hidden.
Disagreements on record (a) Species / mesh. This page uses rat PLCδ1 (1DJX). Human PLCD1 (P51178) has no catalytic PDB; human PLCG1/PLCB1 deposits do not provide this TIM-barrel active site. The chemistry taught is the conserved PLCδ1 phosphodiesterase reaction; the species is stated on screen. (b) Occupancy. 1DJX models the product I3P (IP₃), not PIP₂; the substrate pose is schematic. (c) Nucleophile. The attacking hydroxide is drawn as an explicit O–H (schematic); its position (in-line opposite O11) and protonation state are not resolved by X-rays. (d) The attack is a proposal. The in-line register is a ground-state reconstruction, not a trapped transition state. (e) Catalytic Ca²⁺ required. PLCδ1 is Ca²⁺-dependent; the C2-domain Ca A 3 is shown as context only and is not the catalytic metal. (f) His311 / His356. Assigned as the putative general base / general acid from the literature (Essen et al., Nature 1996 (structure); Biochemistry 1997 (mechanism)) — stated as an assignment, not fact. (g) No protein-domain swing. The PH domain is absent from this construct and no loop motion is modeled.
Regulation — PLCδ1 is Ca²⁺-dependent; PH domain and compartmentation PLCδ1 is a Ca²⁺-activated isozyme. Its N-terminal PH domain binds PtdIns(4,5)P₂ and helps recruit the enzyme to the membrane; the construct on this page (1DJX) is a catalytic-domain deletion variant that lacks the PH domain, so membrane targeting is not shown. Regulation of PLCδ1 is dominated by Ca²⁺ (the catalytic Ca²⁺ plus a C2-domain Ca²⁺), and the enzyme cycles between cytosolic and membrane-bound states. Different PLC families are regulated differently (PLCβ by G-proteins, PLCγ by receptor tyrosine kinases) but share this catalytic chemistry. Together with phosphoinositide kinases and phosphatases, PLC sets the balance of PIP₂, IP₃ and DAG.Source: UniProt P10688 · PDB 1DJX
Kinetics scope (no measured timecourse on this page) One hydrolysis event is drawn, not a steady-state run. Compiled BRENDA values for EC 3.1.4.11 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 3.1.4.11 — no k_cat/K_m re-asserted
Sequence Rat PLCδ1 UniProt P10688 · NCBI Gene 25726. Human isozyme PLCD1 = P51178 (no catalytic PDB). Screen uses 1DJX chain A author numbering; modeled author resi 200–756 (PH domain absent). Ca²⁺ ligands Asn312 / Glu341 / Asp343 / Glu390; putative general base His311 and general acid His356; phosphate anchors Arg549 / Lys438 / Ser522.
Simulation map — what you see is what is written Setup = empty 1DJX pocket + catalytic Ca²⁺ (opaque, no autoplay). ① PIP₂ moves in (schematic) with Ca²⁺ / anchor contacts. ② slow-mo: blue Ca²⁺-activated hydroxide (O–H) attacks P1 in-line. ③ slow-mo: P1–O(DAG) breaks; PIP₂ fades to IP₃ + DAG. ④ DAG leaves. ⑤ IP₃ leaves, Ca²⁺ site restored. Only these events move.
Sources — bibliography of this page S1 — PDB 1DJX: phosphoinositide-specific phospholipase C-δ1 from rat complexed with inositol-1,4,5-trisphosphate, 2.30 Å — public coordinates; catalytic Ca²⁺ A 2, product I3P A 1, C2-domain Ca²⁺ A 3. Measured Ca²⁺ ⋯ Glu390 OE1 = 2.28 Å · Ca²⁺ ⋯ Asn312 OD1 = 2.36 Å · Ca²⁺ ⋯ I3P O2 = 2.36 Å · Ca²⁺ ⋯ Asp343 OD2 = 2.44 Å · Ca²⁺ ⋯ Glu341 OE2 = 2.45 Å · Ca²⁺ ⋯ Asp343 OD1 = 2.47 Å; Ser522 OG ⋯ I3P O42 = 2.58 Å · Arg549 NH1 ⋯ I3P O3 = 2.66 Å · His356 NE2 ⋯ I3P O13 = 3.06 Å · His311 NE2 ⋯ I3P O11 = 3.29 Å S2 — Sequence/annotation: UniProt P10688 (rat PLCδ1) · P51178 (human PLCD1, no catalytic PDB) · NCBI Gene 25726 S3 — Mechanism: Essen et al., Nature 1996 / 1997 — His311 putative general base and His356 putative general acid assignment; Ca²⁺-dependent phosphodiesterase chemistry S4 — Kinetics: BRENDA EC 3.1.4.11 — 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., the PIP₂ substrate, the DAG leaving group, the catalytic hydroxide (drawn as O–H) and the in-line attack), the pose is drawn schematically and labeled as such in the narration.

PLCδ1 catalytic domain (TIM barrel)PLCδ1 C2 domainCa²⁺ONPnucleophile (blue)