Abstract
We have determined X-ray crystal structures of four members of an archaeal specific family of proteins of unknown function (UPF0201; Pfam classification: DUF54) to advance our understanding of the genetic repertoire of archaea. Despite low pairwise amino acid sequence identities (10–40%) and the absence of conserved sequence motifs, the three-dimensional structures of these proteins are remarkably similar to one another. Their common polypeptide chain fold, encompassing a five-stranded antiparallel β-sheet and five α-helices, proved to be quite unexpectedly similar to that of the RRM-type RNA-binding domain of the ribosomal L5 protein, which is responsible for binding the 5S- rRNA. Structure-based sequence alignments enabled construction of a phylogenetic tree relating UPF0201 family members to L5 ribosomal proteins and other structurally similar RNA binding proteins, thereby expanding our understanding of the evolutionary purview of the RRM superfamily. Analyses of the surfaces of these newly determined UPF0201 structures suggest that they probably do not function as RNA binding proteins, and that this domain specific family of proteins has acquired a novel function in archaebacteria, which awaits experimental elucidation.
Highlights
IntroductionUnderstanding the origins of and evolutionary relationships among the three domains of life (archaea, eubacteria, and eukaryotes) constitutes one of the great challenges for postgenomic biology
Understanding the origins of and evolutionary relationships among the three domains of life constitutes one of the great challenges for postgenomic biology
Analyses of the surfaces of these newly determined UPF0201 structures suggest that they probably do not function as RNA binding proteins, and that this domain specific family of proteins has acquired a novel function in archaebacteria, which awaits experimental elucidation
Summary
Understanding the origins of and evolutionary relationships among the three domains of life (archaea, eubacteria, and eukaryotes) constitutes one of the great challenges for postgenomic biology. Better known archaebacteria include Methanococcus jannaschii, Sulfolobus solfataricus, Archaeoglobus fulgidus, and Methanobacterium thermoautotropicum These organisms are each members of the two major archaeal groups, namely crenarchaeota and euryarchaeota, defining all the basic molecular life machinery [5,15,16]. The New York SGX Research Center for Structural Genomics (NYSGXRC; www.nysgxrc.org) targeted four archaeal specific, UPF0201 family proteins for structural characterization and functional annotation, from among thermoacidophiles and hyperthermophiles (both methanogens), representing the two major archaeal phyla crenarchaeota and euryarchaeota [5,15,16]. Analyses of the surfaces of these newly determined UPF0201 structures suggest that they probably do not function as RNA binding proteins, and that this domain specific family of proteins has acquired a novel function in archaebacteria, which awaits experimental elucidation
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