The two-domain multicopper oxidases are proposed to be key intermediates in the evolution of three-domain multicopper oxidases. A number of two-domain multicopper oxidases have been identified from genome sequences and are classified as type A, type B, or type C on the basis of the predicted location of the type 1 copper center. The crystal structure of blue copper oxidase, a type C two-domain multicopper oxidase from Nitrosomonas europaea, has been determined to 1.9 Å resolution. Blue copper oxidase is a trimer, of which each subunit comprises two cupredoxin domains. Each subunit houses a type 1 copper site in domain 1 and a type 2/type 3 trinuclear copper cluster at the subunit-subunit interface. The coordination geometry at the trinuclear copper site is consistent with reduction of the copper ions. Although the overall architecture of blue copper oxidase is similar to nitrite reductases, detailed structural alignments show that the fold and domain orientation more closely resemble the three-domain multicopper oxidases. These observations have important implications for the evolution of nitrite reductases and multicopper oxidases.
Multicopper oxidases (MCOs)2 are a widely distributed class of enzymes with diverse functions ranging from copper and iron metabolism to polyphenol oxidation. MCOs contain four copper ions arranged in two sites: a blue type 1 mononuclear copper center (T1) and a trinuclear copper cluster (T2/T3) consisting of a normal type 2 copper center (T2) and dinuclear type 3 (T3) center (1-3). Substrate oxidation is coupled to reduction of dioxygen to water via electron transfer from the T1 site to the T2/T3 cluster where dioxygen binds (4, 5). Because of structural similarities, MCOs are often grouped with copper nitrite reductases (NIRs), which contain both T1 and T2 sites (6), and are collectively referred to as multicopper blue proteins (MCBPs) (7). MCOs are composed of multiple cupredoxin domains, and both three-domain and six-domain variants have been studied. Three-domain MCOs (3dMCOs) include ascorbate oxidase, laccases, CueO, and Fet3. In these proteins, the T1 site is located in the C-terminal cupredoxin domain, and the T2/T3 cluster is located at the interface between domains 1 and 3 (8, 9). Ceruloplasmin is a six-domain MCO that houses T1 sites in domains 2, 4, and 6 and a T2/T3 cluster between domains 1 and 6 (10).Because of the prevalence of cupredoxin domains, blue copper proteins, and MCOs in nature, understanding their origins has the potential for addressing important questions about the evolution of protein size, function, structure, and complexity (11). Several models for the evolution of three-and six-domain MCOs have been proposed. In these models, the key evolutionary intermediates are two-domain ancestral MCOs (7,11,12). The two-domain MCOs (2dMCOs) are hypothesized to result from a single domain duplication event and have architectures resembling the homotrimeric two-domain NIRs. NIRs contain a T1 site in each domain 1 and a T2 site at the intersubunit interfaces betwee...