A PilT N-terminus domain protein SSO1118 from hyperthemophilic archaeon Sulfolobus solfataricus P2

Abstract

The PilT N terminus (PIN) domains with about 130 amino acids in length comprise a very large protein family present in all three kingdoms of life (Arcus et al. 2011). In the Pfam database, the PIN-domain family (PF01850) currently contains 8,807 members from bacteria, archaea, and eukaryotes. The biological functions of PIN-domains are diverse in various species. Most PIN domains have ribonuclease activity involved in different biological process. In eukaryotes, PIN domains are involved in nonsense mediated mRNA decay (NMD), RNA interference (RNAi), ribosomal RNA processing, and RNA degradation in immune response regulation (Bleichert et al. 2006; Xu et al. 2012). In prokaryotes, the majority of PIN domain proteins are the toxic components of VapBC-type toxinantitoxin systems for stress response, while the toxic activity comes from their nuclease activity (Arcus et al. 2011; Blower et al. 2011). Recently, PIN domains were found in Chp1 of RITS (the RNA-induced initiation of transcriptional gene silencing) complex (Schalch et al. 2011) and Rrp44 in the yeast exosome (Makino et al. 2013). PIN-domains have poor sequence conservation but a conserved three-dimensional structure (Arcus et al. 2011). As is shown by the determined structures of many PINdomain proteins using X-ray crystallography, PIN-domains from various organisms have a 3-layer a/b/a sandwich structure which contains a 5-stranded parallel b-sheet with the order 32145 (Arcus et al. 2011). The revealed structural fold of PIN-domains has significant similarity with the Rossmann fold, a nucleotide-binding module existing in many dehydrogenases, kinases, and flavodoxins (Rossmann et al. 1974). Besides the conserved core structure, PINdomain proteins often contain structural decorations and variations of loop and secondary structure elements, such as different a-helix orientation, different length of b-stand, and additional a-helix or b-stand (Takeshita et al. 2007; Bunker et al. 2008). Despite the poor sequence conservation, PIN domains contain a highly conserved active site constituted by several acidic residues for metal binding and ribonuclease activity (Arcus et al. 2011). Protein SSO1118 with the full length of 111 residues from hyperthermophilic archaeon Sulfolobus solfataricus P2 was annotated as a hypothetical protein conserved in Sulfolobale (Fig. 1a). Our previous sequence analysis and NMR chemical shift assignment studies suggested that SSO1118 is a novel putative PIN domain protein (Xuan et al. 2011). Most archaeal PIN domains are from VapC gene of VapBC toxinantitoxin pair whose genes are in an operon in genome, but the gene of SSO1118 is alone in the genome of S. solfataricus P2. Blast search in PDB does not give significant hit. This indicates that SSO1118 has no significant homology with structure-known proteins. In the present study, the solution structure of SSO1118 was determined by NMR J. Xuan (&) X. Song Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China e-mail: jsxuan@sas.ustb.edu.cn