Get To Know Histidine

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Get To Know Histidine

A versatile, important, and confusing amino acid.

Gale Rhodes
Chemistry Department
University of Southern Maine

The Active Site of Malate Dehydrogenase

In the conversion of malate to oxaloacetate, it is proposed that histidine acts as a general base, abstracting the proton from the hydroxyl of malate (MLT313), and driving the transfer of a hydride ion (not shown) onto the nicotinamide ring of NAD+ (below malate). If the proposal is correct, then before the proton transfer, the histidine ring is in the neutral imidazole form, tautomer C in the figure below. Proton transfer converts the ring to the imidazolium ion (resonance hybrid B).

Convergent stereo image, prepared with DeepView.

Physiologically IMPORTANT Ionization States of the Histidine Side Chain

Ionic and Tautomeric States of the Histidine Side Chain


The side chain of histidine includes the ionizable imidazole ring. The pKa value for the ring is approximately 7.0, so at physiological pH, both the acid and base forms are present. The acid form, the imidazolium ion B, is a resonance hybrid of two practically equivalent contributing forms (remember that these two contributors represent one structure). Either of the two ring nitrogens can release a proton (H+) to produce the conjugate base form, imidazole (A or C). Release of proton from the upper nitrogen of B produces the imidazole tautomer A, and release of proton from the lower nitrogen produces imidazole tautomer C. The tautomers equilibrate by way of the protonated form B. At pH values near 7, all three forms, A, B, and C, are present in equilibrium.

Because the acid form, imidazolium B, is a hybrid of the two contributors, it is plausible to show release of a proton from either nitrogen atom in proposing a reaction mechanism involving the imidazolium form as a general acid. Because the base form, imidazole, exists as two equilibrating tautomers A and C, it is plausible to write either tautomer in proposing a reaction mechanism involving the imidazole form as a general base.

A Physiologically RARE Ionization State of Histidine

The Imidazolate Ion


Abstraction of a proton from imidazole (A or C) results in the imidazolate ion D, a resonance hybrid of two practically equivalent contributors. The pKa of imidazole itself is 14.58*, so the pKa of imidazole in a histidine residue of a protein should be near this value. Thus this ionization, producing a free imidazolate ion, would not occur under physiological conditions. In proposing a reaction mechanism for a physioligical process, it is not plausible to propose loss of a proton from an imidazole tautomer (A or C) to form a free imidazolate ion D. Any proposal of free imidazolate ion as an intermediate in an enzymatic reaction is simply incorrect.

Imidazolate ion can be produced in organic solvents by the action of strong irreversible bases, such as hydride ion. The ion can also serve as a ligand in transition-metal complexes.

Thanks to Professor Daryl Eggers of San Jose State University for pointing out to me that imidazolate ion makes at least one appearance in biology, in the histidine side chain that bridges copper and zinc ions in the enzyme copper-zinc superoxide dismutase. Mutations in this enzyme can lead to amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig’s disease. The bridging histidine is shown in the illustration below.

Imidazolate Ion in a Biological SettingMetal-bridging imidazolate in human Cu-Zn superoxide dismutase (1hl5.pdb).
The side chain of histidine 63 appears to be an imidazolate ion, in which both protons of
imidazolium ion are replaced by strong Lewis acids, copper (I or II) and zinc (II) ions.


*The Chemistry of Heterocycles : Structure, Reactions, Syntheses, and Applications, 2nd edition, Theophil Eicher and Siegfried Hauptmann, New York: John Wiley and Sons, 2003, page 166.