All in the family: Structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly

Abstract

The crystal structures of three proteins of diverse function and low sequence similarity were analyzed to evaluate structural and evolutionary relationships. The proteins include a bacterial bleomycin resistance protein, a bacterial extradiol dioxygenase, and human glyoxalase I. Structural comparisons, as well as phylogenetic analyses, strongly indicate that the modem family of proteins represented by these structures arose through a rich evolutionary history that includes multiple gene duplication and fusion events. These events appear to be historically shared in some cases, but parallel and historically independent in others. A significant early event is proposed to be the establishment of metalbinding in an oligomeric ancestor prior to the first gene fusion. Variations in the spatial arrangements of homologous modules are observed that are consistent with the structural principles of three-dimensional domain swapping, but in the unusual context of the formation of larger monomers from smaller dimers or tetramers. The comparisons support a general mechanism for metalloprotein evolution that exploits the symmetry of a homooligomeric protein to originate a metal binding site and relies upon the relaxation of symmetry, as enabled by gene duplication, to establish and refine specific functions.Keywords: bleomycin resistance protein; extradiol dioxygenase; glyoxalase I; metalloproteins; modular proteins; protein evolution; three-dimensional domain swapping Gene duplication is recognized as a primary mechanism for the origination of new functions during the course of evolution. Indeed, numerous analyses of the sequences and tertiary structures of proteins have revealed the duplication, and, in some cases the subsequent fusion, of genes that code for protein modules. Recognized families of proteins derived from duplicated genes tend to have shared or closely related functions because identification by sequence analysis is limited to cases where the primary structures

Microbial Relatives of the Seed Storage Proteins of Higher Plants: Conservation of Structure and Diversification of Function during Evolution of the Cupin Superfamily

“…The discovery of the cupin superfamily epitomizes the value of an integrated approach to the study of protein structure and function (24,38,119,286). Only by such integration of information available from the previous X-ray analysis of storage proteins (155,177) with data from the prokaryotic genome programs was it possible to detect the evolutionary connection between this wide spectrum of enzymes and binding proteins and thereby to reinforce the concept that there is only a relatively small number of structurally conserved elements from which all proteins are constructed (271).…”

Glyoxalase biochemistry

“…Recent reports have identified additional Ni 2+ -activation class Glo1 enzymes in plant systems, including single subunit enzymes of the same size as the S. cerevisiae and the P. falciparum Glo1 (76-79). These findings are being actively studied with respect to stress response systems in agricultural important crops, and should prove extremely important in addressing the An additional aspect to the overall molecular structure of the Glo1 enzymes is that their protein fold is shared by other proteins in its structural class (βαβββ structural superfamily) yet these proteins exhibit a range of biological activities (54,80,81). Each protein subunit from a homodimeric Glo1 enzyme such as that from H. sapiens or E. coli is composed of two βαβββ structural domains.…”

“…For the extended single chain Glo1 from S. cerevisiae and P. falciparum, based on protein homology modeling, four βαβββ domains are likely present. It has been proposed that the evolution of new structures and functions within this protein family likely arose from a combination of horizontal gene transfer and gene fusion events and possibly gene duplication events (79,81). The possibility of three-dimensional domain swapping has also been proposed (52,54).…”

1.6 Å Crystal structure of a PA2721 protein from pseudomonas aeruginosa—A potential drug‐resistance protein

“…For example, the residues involved in Fe ϩ2 coordination in extradiol dioxygenase (E.C.1.13.11.39) (H146, H210, and E260) superimposed within 0.7-1.4 Å (C␣ atoms) of the Zn ϩ2 coordinating residues in glyoxalase I (Q33, E99, H126, E172) (E.C.4.4.1.5). 2,7 However, PA2721 is unlikely to bind metal ions because superimposition of PA2721 with these enzymes using the SSM server showed that residues H35, G146, F76, E117 occupy equivalent positions. 8 These residues are unlikely to provide a good environment for metal ion coordination.…”

“…The structure was determined by SAD phasing using autoSHARP and refined against the peak data with REFMAC5. 2,15 The initial model was autotraced with 1.6 Å data using the program ARP/wARP. 16 The partial model obtained from ARP/wARP was subsequently manually extended, and rebuilt with O and COOT.…”