UPF201 Archaeal Specific Family Members Reveal Structural Similarity to RNA-Binding Proteins but Low Likelihood for RNA-Binding Function

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.

Expression, purification and structural analysis of the Pyrococcus abyssi RNA binding protein PAB1135

“…Interestingly, and similar to Pyrococcus abyssi, the gene encoding the Archaeoglobus fulgidus Af2318 protein is present in the same operon as RNase P subunit Rpp30 [ 7 ]. Sequence analysis has led to the clustering of these proteins in the UPF0201 family [ 17 ]. The structures of members of this protein family show a single α/β domain characterized by a twisted five-stranded anti parallel β-sheet with five α-helices on one side and an unprotected concave surface of the sheet on the other side [ 17 ].…”

“…Sequence analysis has led to the clustering of these proteins in the UPF0201 family [ 17 ]. The structures of members of this protein family show a single α/β domain characterized by a twisted five-stranded anti parallel β-sheet with five α-helices on one side and an unprotected concave surface of the sheet on the other side [ 17 ]. A homology model of the PAB1135 based on 2OGK presents good stereochemistry as judged by PROCHECK and VERIFY-3D.…”

“…MODELLER [[ 16 ], version 9v1] was used to produce a homology molecular model of PAB1135. The structure of the conserved hypothetical protein Af2318 from Archaeoglobus fulgidus (PDB code 2OGK , [ 17 ]) was used as a template. This protein shares 40% identity with the PAB1135 sequence, being the top hit in a search through the PDB [ 18 ] using BLAST [ 19 ].…”

“…The analysis was made through visualization of the superimposed structures using PYMOL [ 23 ] and various alignments produced with CLUSTALX. COOT [ 24 ] was used for the superposition [ 25 ] of the atomic coordinates of the models and PDB files: 2OGK [ 17 ], 1JJ2 [ 26 ], and 1MJI [ 27 ]. DALI [ 28 ] was also used for analysis of correlated structures.…”