The rhodanese/Cdc25 phosphatase superfamily. Sequence-structure-function relations

Abstract

Rhodanese domains are ubiquitous structural modules occurring in the three major evolutionary phyla. They are found as tandem repeats, with the C-terminal domain hosting the properly structured active-site Cys residue, as single domain proteins or in combination with distinct protein domains. An increasing number of reports indicate that rhodanese modules are versatile sulfur carriers that have adapted their function to fulfill the need for reactive sulfane sulfur in distinct metabolic and regulatory pathways. Recent investigations have shown that rhodanese domains are also structurally related to the catalytic subunit of Cdc25 phosphatase enzymes and that the two enzyme families are likely to share a common evolutionary origin. In this review, the rhodanese/Cdc25 phosphatase superfamily is analyzed. Although the identification of their biological substrates has thus far proven elusive, the emerging picture points to a role for the amino-acid composition of the active-site loop in substrate recognition/specificity. Furthermore, the frequently observed association of catalytically inactive rhodanese modules with other protein domains suggests a distinct regulatory role for these inactive domains, possibly in connection with signaling.

Fig. 1. Scheme representing the sulfur-transfer reaction catalyzed by rhodanese.

Fig. 2. Three-dimensional structure of A. vinelandii RhdA and of human Cdc25A phosphatase, superimposed on their respective catalytic domains. RhdA and Cdc25A are shown in blue and yellow, respectively. Active-site loops and the structurally equivalent loop on the RhdA N-terminal domain are shown in red. The catalytic Cys and the Asp counterpart on the inactive domain are represented in ball-and-stick. Conserved residues, Tyr37 and His41 (RhdA numbering), putatively involved in regulative function (see text) are also shown. The linker polypeptide connecting the two RhdA domains is shown in pink. The βC–αC loops involved in RhdA in interdomain interaction (Bordo et al., 2000) are shown in green.

Fig. 3. Neighbor-joining tree representing the rhodanese superfamily generated by CLUSTALW (correction for multiple substitution was adopted; Thompson et al., 1997). The multiple alignment was derived from that included in the SMART resource, to which four E. coli, two archaea and two ThiI proteins were added, for a total of 155 rhodanese modules. The SMART alignment represents an even sample of the total number of rhodanese modules, as closely related sequences are represented only once. The tree was displayed and validated by bootstrap analysis using programs in the PHYLIP package (Felsenstein, 1989). Archaeal, bacterial and eukaryotic proteins are represented in blue, red and green, respectively. Symbols are used to indicate the distinct structural or functional roles of the rhodanese modules, as described in the inset.

Fig. 4. Co-occurrence of rhodanese modules in association with other protein domains. Domains are schematized as colored boxes. Catalytic rhodanese modules with a six-amino-acid active-site loop are shown in red, and inactive rhodanese modules are displayed in black. Rhodanese modules with a seven-amino-acid active-site loop are displayed in yellow. Other protein domains are shown in gray. Active-site loop positions displaying at least 80% amino-acids conservation within each subfamily are also shown as conserved motifs.

Domenico Bordo & Peer Bork