Pyruvate Carboxylase - 3D Mechanism Simulator

Loading structural data… (3BG3)

References & Databases

START HERE — how to read pyruvate + carboxybiotin → OAA + biotin A single carboxyl-transfer cartoon on the human PC CT pocket that actually exists: 3BG3 (2.80 Å), a BC-deleted fragment (CT+PT+BCCP). Real crystal: pyruvate, Mn²⁺, carbamylated Lys741 (KCX), and a BCCP BTI analog on Lys1144. The CT carboxyl donor is schematic carboxybiotin — BTI is ~75–80 Å away on BCCP, not this chemistry. Thr908 ★ is the C3 general base (OG1⋯CB = 3.12 Å). Gold H⁺ parks on Thr908; pyruvate fades to schematic oxaloacetate. The BC half (ATP + HCO₃⁻) is missing. Two-crystal / analog distances that are not deposited on this frame are not geomClaims.
Crystal structures PDB 3BG3 — human PC CT+PT+BCCP, 2.80 Å, pyruvate + Mn + BTI + KCX (Xiang & Tong 2008). Coordinates are public. 3BG5 is S. aureus, not this mesh. 7WTE/7WTA are full-length EM with acetyl-CoA (allosteric story). 8XL9 title says human PC but the primary citation is PCC/MCC — not used.
Mechanism — CT carboxyl transfer; BC half absent Xiang & Tong, Nat Struct Mol Biol 2008, PMID:18297087 — carboxyltransfer on this fragment. UniProt P11498 EC 6.4.1.1: HCO₃⁻ + pyruvate + ATP → OAA + ADP + Pi + H⁺. This page implements the CT half only. Thr908 OG1 faces pyruvate C3. Mn²⁺ is held by KCX741 / Asp572 / His773 / His771. Source: Xiang 2008 · UniProt P11498
0 — Setup: Mn²⁺ + BTI, CT pocket shown empty 3BG3 holds pyruvate, Mn, KCX, and BTI. The CT pocket is shown empty so ordered binding can start. Mn²⁺ stays as the Lewis-acid occupant. BTI stays on BCCP as a named analog — it is not the CT donor. Opaque, run:null (no autoplay). Thr908 ★ faces C3. The BC domain is missing.Source: PDB 3BG3
① — Pyruvate binds (crystal) Crystal pyruvate docks. PDB names: C = C1 carboxyl, CA = C2, CB = C3 methyl, O3 = C2=O. Thr908 OG1 ⋯ CB = 3.12 Å on this deposit. Arg644 NE ⋯ O = 2.63 Å. Binding order is compiled staging, not a fit.Source: 3BG3 PYR A2000 pose
② — Carboxybiotin presented (schematic) Schematic carboxybiotin is seated in the CT pocket — not deposited BTI. BTI is a biotin aldehyde covalently on Lys1144 of BCCP, far from pyruvate. The BC half that carboxylates biotin is absent.Source: Xiang 2008 CT chemistry · 3BG3 BTI occupancy named, not used as donor
③ — Thr908 ★ abstracts the C3 proton (hypothetical, lit.-based) A gold H⁺ sphere rides a gold arrow from pyruvate CB to Thr908 OG1 and parks. The enolate label is a teaching overlay. Xiang 2008 writes this enolization with carboxyl transfer; this page splits them.Source: Xiang 2008 · 3BG3 Thr908⋯CB 3.12 Å
④ — Carboxyl transfer → oxaloacetate (hypothetical, lit.-based) The C3 enolate attacks schematic carboxybiotin CX. Pyruvate fades in place to schematic OAA; carboxybiotin fades to biotin. Parked gold H⁺ stays on Thr908. Schematic CX⋯CB is a teaching stitch, not a measured transfer Å. Slow-motion on purpose.Source: compiled PC CT · UniProt P11498 OAA product
⑤ — Thr908 regenerates — not the net H⁺ (hypothetical, lit.-based) The parked gold H⁺ leaves OG1. This is CT-base recycle, not the net H⁺ of EC 6.4.1.1 (that proton is the BC half, absent here).Source: EC 6.4.1.1 net H⁺ is BC, not CT
⑥ — OAA leaves — PEPCK is next [schematic] Oxaloacetate departs. Schematic biotin stays in the CT pocket as a tethered prosthetic — it is not a free cofactor flying away. Mn²⁺ and BCCP BTI stay. OAA is the substrate of cytosolic PEPCK. ADP+Pi are not this pocket.Source: GNG bookkeeping

How to read this page — a first-pass primer First pass: Setup (Mn²⁺ + BTI present, CT pocket empty, Thr908 ★, BC missing) → ① pyruvate docks → ② schematic carboxybiotin docks → ③ gold H⁺ CB → OG1 (parks) → ④ carboxyl CX → C3, pyruvate becomes OAA → ⑤ gold H⁺ leaves (not net H⁺) → ⑥ OAA leaves (biotin stays tethered). Second pass: 3.12 Å is a crystal fact on 3BG3; carboxybiotin, OAA, and the H sphere are [schematic]. Third pass: open “Disagreements” for BC-missing, BTI vs CBI, and concerted vs split.
Chemistry primer — two-half biotin carboxylase PC is a biotin-dependent ligase. The BC domain carboxylates biotin-Lys1144 with ATP + HCO₃⁻. The CT domain then transfers that carboxyl onto pyruvate C3 to make oxaloacetate. This page is CT only. Gold = H⁺. Mn²⁺ is a Lewis acid, not a redox cofactor. KCX is carbamylated Lys741 in the Mn shell, not free bicarbonate.
Words used on screen — BTI · CBI · KCX · BC missing BTI — deposited biotin aldehyde analog on Lys1144 (BCCP), not the CT donor. CBI — schematic carboxybiotin in the CT pocket. KCX — N6-carboxylysine at 741 (carbamate). BC missing — 3BG3 starts at UniProt 482; ATP-grasp 36–486 is absent.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 3BG3 (2.80 Å) with pyruvate, Mn, KCX, BTI; Thr908 OG1 ⋯ PYR CB = 3.12 Å; Mn shell 1.96–2.29 Å. The inferred layer ([schematic]): carboxybiotin body, OAA, transferring H⁺ sphere, product leave, and ⑤ Thr regeneration. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Schematic contacts are not geomClaims.
Disagreements on record (a) BC domain missing. ATP + HCO₃⁻ chemistry is not on this mesh. (b) BTI ≠ CT donor. BTI is BCCP-tethered ~75–80 Å from pyruvate; CBI is schematic. (c) Concerted vs split. Compiled PC writes enolization + transfer as one event; this page splits them (③ then ④) for 1-event/1-step teaching. (d) Net H⁺. EC 6.4.1.1 H⁺ is BC, not CT-base recycle. (e) 3BG5 is S. aureus. (f) 8XL9 citation ≠ title (PCC/MCC). (g) 7WTE acetyl-CoA is allosteric, not this motion.
Regulation — acetyl-CoA · biotin · mitochondrial matrix Acetyl-CoA is the classic allosteric activator (7WTE ATP+ACO) — named, not this CT cartoon. Biotin is covalently on Lys1144. The enzyme is mitochondrial matrix (transit 1–20). PC deficiency is a clinical entity — named, not simulated.Source: Chai 2022 PMID:36283412 · UniProt P11498
Kinetics scope (no measured timecourse on this page) One pyruvate → OAA event is drawn, not a steady-state run. Compiled BRENDA values for EC 6.4.1.1 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 6.4.1.1 — no k_cat/K_m re-asserted
Sequence Human PC UniProt P11498 · NCBI Gene 5091. Screen uses 3BG3 / UniProt numbering (Thr908, Lys741, Lys1144). Construct is His-tag + residues 482–1178; BC 36–486 is absent.
Simulation map — what you see is what is written Setup = 3BG3 CT pocket empty, Mn²⁺ + BTI visible (opaque, run:null). ① pyruvate moves in (crystal). ② schematic carboxybiotin moves in. ③ gold H⁺ + gold arrow CB → Thr908 OG1 (parks). ④ slow-mo: carboxyl CX → C3; pyruvate fades to OAA; CBI fades to biotin; parked gold H⁺ remains. ⑤ gold H⁺ leaves OG1 (not net H⁺). ⑥ OAA leaves; schematic biotin stays tethered in the CT pocket; Mn and BTI stay. Only these events move.
Sources — bibliography of this page S1 — PDB 3BG3: human PC CT+PT+BCCP, 2.80 Å, PYR + MN + BTI + KCX — public coordinates; measured OG1⋯CB = 3.12 Å S2 — Xiang & Tong, Nat Struct Mol Biol 2008, PMID:18297087 — carboxyltransfer on this fragment; 3BG5 is S. aureus S3 — Chai et al., Mol Cell 2022, PMID:36283412 — full-length EM / acetyl-CoA (7WTE); allosteric, not this CT cartoon S4 — Sequence: UniProt P11498 (human PC) · NCBI Gene 5091 S5 — Kinetics: BRENDA EC 6.4.1.1 — no k_cat/K_m re-asserted on this page

› 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., carboxybiotin in the CT barrel, OAA identity, H⁺ flight, product release), the pose is drawn schematically and labeled as such in the narration.

CT domainPT + BCCPONH⁺ (gold)