Soluble guanylate cyclase - 3D Mechanism Simulator

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START HERE — how to read GTP → 3′,5′-cGMP + PPi on soluble guanylate cyclase One cyclization cartoon on the human soluble guanylate cyclase (sGC) α1/β1 heterodimer: 6JT2 (cryo-EM 3.80 Å, NO-activated) with the GTP analog G2P = phosphomethylphosphonic acid guanylate ester, two Mg²⁺ and heme b. This is a human enzyme — α1 = GUCY1A1 (UniProt Q02108), β1 = GUCY1B1 (UniProt Q02153). G2P is a non-hydrolyzable analog: its α–β bridge is a methylene carbon (P–CH₂–P), so the β–γ diphosphate cannot leave. The true substrate is GTP; 6JT2 models no cGMP and no PPi, so the cyclic product and the pyrophosphate are [schematic], and the 3′-OH attack is (proposal, lit.-based). The general base is not assigned on this frame. NO is not modeled — the heme on β1 is named only. Resolution hedge: the 3.80 Å EM map is coarse, so measured contacts are approximate. Measured Å are deposited 6JT2 pairs only.
Crystal structure PDB 6JT2 — human soluble guanylate cyclase (sGC α1/β1), NO-activated state, cryo-EM 3.80 Å; coordinates are public. Chain A = human GUCY1A1 (UniProt Q02108, observed 67–659); chain B = human GUCY1B1 (UniProt Q02153, observed 1–606), which carries the heme b (HEM B1000, proximal His105). Deposited ligands: G2P A1001 (GTP analog), two Mg²⁺ (MG A1002 / A1003), and heme. EC 4.6.1.2 (guanylate cyclase / GTP pyrophosphate-lyase, cyclizing). The 3.80 Å resolution is coarse.
Mechanism — 3′-OH attack on the α-phosphate, cGMP + PPi (same cyclase chemistry as adenylyl cyclase) sGC converts GTP to the second messenger 3′,5′-cyclic GMP plus PPi. Like adenylyl cyclase (EC 4.6.1.1), the ribose 3′-OH is the nucleophile that attacks the α-phosphate; the β,γ-diphosphate leaves as PPi. On 6JT2 the deposited ligand is the non-hydrolyzable G2P analog (α–β methylene bridge), so the ring closure is [schematic] / (proposal, lit.-based). The two metals (Mg²⁺ A1002 / A1003, ligated by α1 Asp486 / Asp530) are the deposited Lewis acids; α1 Arg574 and β1 Arg552 stabilise the transition state and β1 Glu473/Arg552 recognise the guanine (literature-based). Source: PDB 6JT2 · UniProt Q02108 / Q02153 · BRENDA EC 4.6.1.2
0 — Setup: empty sGC cleft + two Mg²⁺ + heme named 6JT2 holds the nucleotide site with Mg²⁺ (A1002 / A1003) (Asp486 / Asp530 ligands) and the heme b on β1 (HEM B1000, proximal His105) as named context. The pocket is shown empty so binding can start; 6JT2 models no cGMP and no PPi. Opaque, no autoplay. NO is not modeled. The chemistry below is schematic. Source: PDB 6JT2
① — G2P (GTP analog) binds The crystal nucleotide G2P docks into the α1/β1 cleft — a non-hydrolyzable GTP analog, not GTP itself; the true substrate is GTP. Measured register: Arg552 NH2 ⋯ O2A = 2.37 Å, Gly489 N ⋯ O3G = 2.44 Å, Arg574 NH2 ⋯ O1G = 2.56 Å, Phe490 N ⋯ O1B = 2.71 Å, Asp486 OD2 ⋯ O1G = 2.74 Å, Asp530 OD2 ⋯ O2B = 2.75 Å, Glu473 OE1 ⋯ O6 = 2.94 Å, and the Mg site MG ⋯ O2B = 1.98 Å / MG ⋯ O5′ = 2.17 Å.Source: measured 6JT2 pairs (3.80 Å EM) · PDB 6JT2
② — 3′-OH is deprotonated (general base unassigned) (hypothetical, lit.-based) Gold H⁺ leaves the ribose 3′-OH; the base is not assigned on this frame (the metals and the Arg574/Arg552 network position and stabilise, they are not shown as the base). The remaining 3′-O⁻ is the alkoxide nucleophile. Slow-motion on purpose.Source: compiled cyclase chemistry · 6JT2 geometry
③ — 3′-O⁻ attacks Pα → 3′,5′-cGMP + PPi (hypothetical, lit.-based) Blue 3′-O⁻ attacks the α-phosphate PA; the intact analog cross-fades in place to schematic 3′,5′-cGMP + PPi. The deposited analog is non-hydrolyzable (α–β methylene) and the O3′ ⋯ PA register is ~4.08 Å (not in-line), so this is [schematic]. This is the same cyclase chemistry as adenylyl cyclase. Both metals stay. Slow-motion on purpose.Source: compiled cyclase mechanism · EC 4.6.1.2
④ — PPi leaves [schematic] PPi (β,γ-diphosphate) departs; the new 3′,5′-cGMP stays. Both metals and the heme stay. 6JT2 holds only the intact analog, so PPi is schematic (and the 3.80 Å map is coarse).Source: EC 4.6.1.2 net accounting
⑤ — cGMP leaves — sGC idle, heme/NO named [schematic] 3′,5′-cGMP — the second messenger — departs; the two metals and the cleft are restored. The heme on β1 (proximal His105) is named; NO is not modeled here — NO binding to the heme is the activation step of the NO–sGC pathway, not the catalytic chemistry. Net: GTP → 3′,5′-cGMP + PPi. Products are [schematic].Source: EC 4.6.1.2 net accounting

How to read this page — a first-pass primer First pass: Setup (empty cleft + two Mg + heme named) → ① the GTP analog docks → ② gold H⁺ leaves the 3′-OH → ③ blue 3′-O⁻ attacks Pα, analog → cGMP + PPi → ④ PPi leaves → ⑤ cGMP leaves. Second pass: 1.98 / 2.17 / 2.37 / 2.44 / 2.56 / 2.74 / 2.75 / 2.94 Å are crystal facts on 6JT2 atoms (3.80 Å EM); cGMP, PPi and the deprotonation are [schematic]. Third pass: open “Disagreements” for the coarse EM map, the non-hydrolyzable analog, the unassigned base, the heme on β1, and NO not modeled.
Chemistry primer — cyclizing (GTP pyrophosphate-lyase) sGC is a cyclase, not a hydrolase: the ribose 3′-OH closes a cyclic phosphate onto the α-phosphorus and ejects PPi. Two metal ions (Mg²⁺ A1002 / A1003) hold the phosphates; conserved Arg residues (α1 Arg574, β1 Arg552) stabilise them. Gold = H⁺ on the 3′-OH; blue = the 3′-O⁻ oxygen nucleophile. Teaching substrate = the GTP analog G2P. This is not a phosphodiesterase (that is PDE4, the reverse direction) and it is the same chemistry as adenylyl cyclase with GTP instead of ATP.
Words used on screen — occupancy · G2P · heterodimer · PPi Occupancy — 6JT2 holds the non-hydrolyzable G2P analog at the sGC site; it is never relabeled as GTP or as a transition state. G2P — phosphomethylphosphonic acid guanylate ester: the α–β bridge is a methylene carbon (P–CH₂–P), which blocks hydrolysis. Heterodimer — the mesh joins sGC α1 with sGC β1 (which carries the heme). PPi — the pyrophosphate leaving group.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 6JT2 (cryo-EM 3.80 Å) — MG(A1002) ⋯ G2P O2B = 1.98 Å; MG(A1002) ⋯ Asp486 OD1 = 2.09 Å; MG(A1002) ⋯ Asp486 OD2 = 2.10 Å; MG(A1002) ⋯ Asp530 OD2 = 2.28 Å; MG(A1003) ⋯ G2P O5′ = 2.17 Å; MG(A1003) ⋯ G2P O1A = 2.28 Å; MG(A1003) ⋯ Asp530 OD1 = 2.48 Å; MG(A1003) ⋯ Asp486 OD1 = 2.69 Å; Arg552 NH2 ⋯ G2P O2A = 2.37 Å; Gly489 N ⋯ G2P O3G = 2.44 Å; Arg574 NH2 ⋯ G2P O1G = 2.56 Å; Phe490 N ⋯ G2P O1B = 2.71 Å; Asp486 OD2 ⋯ G2P O1G = 2.74 Å; Asp530 OD2 ⋯ G2P O2B = 2.75 Å; Thr491 N ⋯ G2P O1B = 2.77 Å; Ile487 O ⋯ G2P O2B = 2.85 Å; Ser551 OG ⋯ G2P O2′ = 2.87 Å; Glu473 OE1 ⋯ G2P O6 = 2.94 Å; Lys593 NZ ⋯ G2P O2G = 3.21 Å; Val475 CG1 ⋯ G2P N2 = 3.27 Å; Gly529 CA ⋯ G2P N7 = 3.30 Å; Val488 C ⋯ G2P O3G = 3.33 Å. G2P is a non-hydrolyzable analog. The inferred layer ([schematic]): cGMP, PPi, the 3′-OH deprotonation, and product release. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. The 3.80 Å EM map is coarse, so all contacts are approximate; the general base is not assigned.
Disagreements on record (a) Coarse EM map. 6JT2 is 3.80 Å — atom positions carry real uncertainty, so measured Å are approximate. (b) Non-hydrolyzable analog. G2P has an α–β methylene bridge; the true substrate is GTP, so the cyclization is schematic. (c) No cGMP / no PPi modeled in 6JT2 — both products are schematic. (d) Geometry is not in-line. The O3′ ⋯ PA register is ~4.08 Å — an attack register, not a transition state. (e) General base unassigned. No residue is drawn as the base; the metals/Arg network stabilise only. (f) Heme is on β1. HEM B1000 sits on a different domain from the catalytic site; NO is not modeled, and no NO/heme electron transfer is drawn. (g) Same chemistry as adenylyl cyclase. The cyclization is presented as shared cyclase chemistry; no distinct sGC transition state is claimed. (h) Gaps. Only modeled Cα are drawn; chain gaps are stretched links.
Regulation — NO–heme activation, isozymes Soluble guanylate cyclase is the NO receptor: NO binds the ferrous heme b on β1 (proximal His105), breaking the proximal bond and activating cGMP synthesis up to ~200-fold. This page shows the catalytic chemistry only — NO is not modeled, and the heme is named only. sGC is a cytosolic heterodimer (GUCY1A1/GUCY1B1); the membrane receptor guanylate cyclase GC-C (GUCY2C) is a different gene (a separate enzyme that responds to peptide hormones such as guanylin, not NO). Do not read GC-C regulation onto this page.Source: UniProt Q02108 / Q02153 · PDB 6JT2
Kinetics scope (no measured timecourse on this page) One cyclization event is drawn, not a steady-state run. Compiled BRENDA values for EC 4.6.1.2 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 4.6.1.2 — no k_cat/K_m re-asserted
Sequence Human sGC α1 = GUCY1A1 UniProt Q02108 (chain A) · human sGC β1 = GUCY1B1 UniProt Q02153 (chain B, carries heme b). Screen uses 6JT2 author numbering (chain A 67–659, chain B 1–606). Membrane isozyme GC-C = GUCY2C is a different gene.Source: UniProt Q02108 / Q02153
Simulation map — what you see is what is written Setup = empty 6JT2 sGC cleft + two Mg²⁺ + heme named (opaque, no autoplay). ① G2P analog moves in. ② slow-mo: gold H⁺ leaves the 3′-OH. ③ slow-mo: blue 3′-O⁻ attacks Pα; analog fades to cGMP + PPi. ④ PPi leaves. ⑤ cGMP leaves; metals restored, heme/NO named. Only these events move.
Sources — bibliography of this page S1 — PDB 6JT2: human soluble guanylate cyclase α1/β1, NO-activated, cryo-EM 3.80 Å — public coordinates; measured MG⋯G2P O2B = 1.98 Å · MG⋯G2P O5′ = 2.17 Å · MG⋯Asp486 OD1 = 2.09 Å · MG⋯Asp530 OD2 = 2.28 Å · Arg552 NH2⋯G2P O2A = 2.37 Å · Gly489 N⋯G2P O3G = 2.44 Å · Arg574 NH2⋯G2P O1G = 2.56 Å · Asp486 OD2⋯G2P O1G = 2.74 Å · Glu473 OE1⋯G2P O6 = 2.94 Å · O3′⋯PA = 4.08 Å S2 — Sequence/annotation: UniProt Q02108 (human GUCY1A1, sGC α1) · Q02153 (human GUCY1B1, sGC β1). Membrane isozyme GC-C = GUCY2C, a different gene. S3 — Kinetics: BRENDA EC 4.6.1.2 — 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., 3′,5′-cGMP, PPi, the 3′-OH deprotonation, product release), the pose is drawn schematically and labeled as such in the narration.

sGC α1 (chain A)sGC β1 (chain B)Mg²⁺Fe / Pheme bH⁺ (gold)nucleophile (blue)