Partial metal depletion and "Cd-NMR studies have suggested that the recombinant Cd-containing metallothionein of the sea urchin Strongylocentrutus purpurutus (Cd,-MTA) binds its metal ions in a four-metal (Cd,Cys,,) and a three-metal (Cd,Cys,) cluster associated with the N-terminal and C-terminal halves of the protein, respectively [Wang, Y., Mackay, E. A., Zerbe, O., Hess, D., Hunziker, P. E., Vasak, M. & Kagi, J. H. R. (1995) Biochemistry 34, 7460-74671. This partitioning has now been confirmed by bisecting native Cd,-MTA with subtilisin into products bearing only a single metal-thiolate cluster. Their separation by reverse-phase HPLC and on-line electrospray mass spectrometry in combination with sequence analysis revealed selective cleavage of the protein into a set of N-terminal polypeptides containing 37-39 residues with four Cd ions and a set of C-terminal polypeptides containing 24 and 25 residues with three Cd ions. Thus, sea urchin MTA like its mammalian counterparts is made up of two separate cluster-harboring domains. The fragmentation pattern indicated that the sites of cleavage are located in the peptide loop interspaced between the first two metal-bound cysteine residues of the C-terminal domain. Accordingly, with cleavage, one of the putative nine thiolate ligands of the three-metal cluster was lost to the N-terminal fragment. The coordinational consequences of this repartition were reflected in massive chiroptical changes accompanying the cleavage process. While the liberated N-terminal domain retained the CD profile of the four-metal cluster in the parent protein and thereby indicated preservation of its structure, the CD features attributable to the intact three-metal cluster were largely lost on cleavage. The vanished features bear strong resemblance to the large biphasic ellipticity signal at 250 nm which dominates the CD spectrum of native Cd,-MTA, and allow us thus to attribute this signal to excitonic coupling interactions of Cd-thiolate chromophores in the three-metal cluster.Keywords: recombinant sea urchin metallothionein ; limited proteolysis; mass spectroscopy ; circular dichroism.Metallothioneins (MT) are small proteins with a high cysteine and d'" metal ion content (e.g. Znz+, Cd2+, Hg2 ' and Cu+).They are ubiquitous in the animal kingdom and are thought to play a central role in cellular Zn and Cu metabolism and in the protection from the toxic elements Cd and Hg (Kagi, 1991; Roesijadi, 1993). The metal ions are bound to the cysteine side chains and "'Cd-NMR studies of MT whose binding sites were fully occupied by "'Cd indicated that both in mammalian and in crustacean MT the metal complexes are joined to form two distinct metal-thiolate clusters (Otvos and Armitage, 1980;Otvos et al., 1982;Frey et al., 1985). This structure was subsequently confirmed by two-dimensional NMR and by X-ray crystallographic studies (Wuthrich, 1991 ;Robbins et al., 1991). Mammalian MT contain a M:+Cys,, and a M,2+CysI, cluster located in the interior of the essentially globular N-terminal and C-termina...