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Function, Structure, and Evolution of the RubisCO-Like Proteins and Their RubisCO Homologs

Department of Microbiology and Plant Molecular Biology/Biotechnology Program, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210-1292,¹ Graduate College of Marine and Earth Studies, Delaware Biotechnology Institute, University of Delaware, 127 DBI, 15 Innovation Way, Newark, Delaware 19711,² Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, Box 951570, Los Angeles, California 90095-1570,³ Department of Plant Cellular and Molecular Biology, The Ohio State University, 582 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, Ohio 43210-1292⁴

Summary: About 30 years have now passed since it was discovered that microbes synthesize RubisCO molecules that differ from the typical plant paradigm. RubisCOs of forms I, II, and III catalyze CO₂ fixation reactions, albeit for potentially different physiological purposes, while the RubisCO-like protein (RLP) (form IV RubisCO) has evolved, thus far at least, to catalyze reactions that are important for sulfur metabolism. RubisCO is the major global CO₂ fixation catalyst, and RLP is a somewhat related protein, exemplified by the fact that some of the latter proteins, along with RubisCO, catalyze similar enolization reactions as a part of their respective catalytic mechanisms. RLP in some organisms catalyzes a key reaction of a methionine salvage pathway, while in green sulfur bacteria, RLP plays a role in oxidative thiosulfate metabolism. In many organisms, the function of RLP is unknown. Indeed, there now appear to be at least six different clades of RLP molecules found in nature. Consideration of the many RubisCO (forms I, II, and III) and RLP (form IV) sequences in the database has subsequently led to a coherent picture of how these proteins may have evolved, with a form III RubisCO arising from the Methanomicrobia as the most likely ultimate source of all RubisCO and RLP lineages. In addition, structure-function analyses of RLP and RubisCO have provided information as to how the active sites of these proteins have evolved for their specific functions.

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