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Indole-3-acetate is the conjugate base of indole-3-acetic acid, formed by loss of a proton from its carboxylic acid group. ChEBI records molecular formula ${\mathrm{C}}_{10}{\mathrm{H}}_8\mathrm{N}{\mathrm{O}}_2^{-}$ and charge $-1$. The uncharged acid and its anion have related chemical roles but are distinct protonation forms.^[ref]

Write the acid as $\mathrm{HA}$ and indole-3-acetate as ${\mathrm{A}}^{-}$:For a dilute two-form model, the Henderson-Hasselbalch equation gives $r=[{\mathrm{A}}^{-}]/[\mathrm{HA}]=10^{\mathrm{pH}-\mathrm{p}{K}_a}$, and the anion fraction is $r/(1+r)$. At pH equal to $\mathrm{p}{K}_a$, the two fractions are equal. One pH unit above it gives $10/11\approx 90.9\%$ anion, while one unit below gives $1/11\approx 9.1\%$. This is a symbolic calculation relative to the acid dissociation constant, not a claim of a newly measured numerical $\mathrm{p}{K}_a$.

The fraction does not specify the total amount. A hypothetical100-nanomole pool in the90.9percent case contains about90.9 nanomoles of indole-3-acetate and9.1 nanomoles of acid. Specifying pH alone would not determine that pool size, a transport rate or a growth response to auxin.

Indole-3-pyruvate is the indole-substituted pyruvate anion named systematically 3-(1H-indol-3-yl)-2-oxopropanoate. It is the conjugate base of indole-3-pyruvic acid. The three-carbon side chain distinguishes it from indole-3-acetate, whose corresponding side chain has two carbons.^[ref]

A biological example is the plant route from tryptophan to the auxin indole-3-acetate. A transamination supplies indole-3-pyruvate; a YUCCA flavin monooxygenase then participates in its conversion to indole-3-acetate. The accepted net reaction uses NADPH and molecular oxygen and releases carbon dioxide, so the step is not simply a change in protonation.^[ref]

An original carbon inventory makes the one-carbon loss clear. The indole framework contributes eight carbon atoms, giving eleven in indole-3-pyruvate and ten in indole-3-acetate. Converting 20 nmol of substrate according to the stated reaction distributes $20(11)=220$ nmol of carbon atoms between $20(10)=200$ nmol in the organic product and 20 nmol in carbon dioxide. The balance checks the net stoichiometry, without establishing the provenance of individual oxygen atoms or a reaction rate.

Indole-3-pyruvic acid is an indole-substituted oxo carboxylic acid, systematically 3-(1H-indol-3-yl)-2-oxopropanoic acid. Its neutral molecular formula is ${\mathrm{C}}_{11}{\mathrm{H}}_9\mathrm{N}{\mathrm{O}}_3$. Its conjugate base is indole-3-pyruvate, which retains the same carbon skeleton after loss of a proton.^[ref]

The acid/base relationship can be represented asBoth sides have eleven carbon atoms and three oxygen atoms; the change concerns protonation and charge. This is different from the biochemical conversion of indole-3-pyruvate to indole-3-acetate, which releases carbon dioxide and changes the carbon inventory of the organic product.^[ref]

An illuminating comparison is therefore between changing a solution's acid/base conditions and changing a metabolite's carbon skeleton. Those operations can alter names or measured signals for different reasons. Identifying the chemical structure and protonation state prevents the acid, its anion and the shorter-side-chain auxin product from being treated as one interchangeable chemical identity.

A YUCCA flavin monooxygenase is a member of a plant enzyme family involved in auxin biosynthesis. Its indole-3-pyruvate monooxygenase activity converts indole-3-pyruvate to indole-3-acetate, the conjugate base of indole-3-acetic acid, with loss of carbon dioxide. The official reaction is EC 1.14.13.168.^[ref]

Let IPyA and IAA denote the two anionic organic participants in that reaction. The net balance isThe reaction uses NADPH and oxygen. Together with an upstream transamination step, it connects tryptophan to indole-3-acetic acid. The net transformation removes one carbon from the substrate's side chain; it does not merely change the substrate's concentration without changing its chemical identity.^[ref]

In a constructed ideal inventory, 40 nanomoles of indole-3-pyruvate, 20 of NADPH and 30 of oxygen permit at most 20 nanomoles each of indole-3-acetate and carbon dioxide through the stated reaction. That ceiling assumes no replenishment or side reactions; donor oxidation alone would not identify the organic product.

A developmental experiment supplies a different kind of evidence. In the parasitic plant Phtheirospermum japonicum, local YUC3 expression and altered gene expression were associated with changes in haustorium development. Such observations connect local auxin production to organ development, while a biochemical assay asks which reaction the enzyme performs.^[ref]