Predicting the Zn(II) Ligands in Metalloproteins: Case Study, Porphobilinogen Synthase

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Abstract
Mammalian porphobilinogen synthase (PBGS) is a Zn(II) metalloenzyme containing both catalytic and non-catalytic Zn(II). There are sufficient physical and chemical data to establish the types of amino acid which serve as ligands to each of the metal ions. Chemical modification data allow specific sequence assignment of some of the Zn(II) ligands. This Comment attempts the prediction of the remaining amino acids which act as Zn(II) ligands. The predictions are based on published Extended X-ray Absorption Fine Structure data, the sequences of PBGS from eleven different species, and an analysis of twenty-four known X-ray and NMR determined structures for proteins which contain Zn(II). The analysis of the known structures follows the precedent set by B. L. Vallee and D. S. Auld (Biochemistry 29 5647–5659 (1990), with the current dataset being ca. 50% larger. Non-catalytic Zn(II) sites are all found to contain a tetrahedral coordination of at least two, and often four, cysteine ligands. In all cases, two of the cysteines are separated by fewer than four intervening amino acids. All six of the structures analyzed show the non-catalytic Zn(II) ligands to be derived from a continuous sequence of up to 35 amino acids. Contrary to the original conclusions of Vallee and Auld, the nineteen catalytic Zn(II) are found to be both tetrahedral and pentacoordinate, and need not contain water as a ligand. The most common catalytic Zn(II) ligand is histidine, and the ligand preference series appears to be H > E = D > C = Y = K = backbone carbonyl. In all cases, except alcohol dehydrogenase, two of the catalytic Zn(II) ligands are separated by no more than three intervening amino acids.