Crystal structures of two archaeal Pelotas reveal inter-domain structural plasticity Hyung Ho Lee a, * , Jun Young Jang b , Hye-Jin Yoon b , Soon Jong Kim c , Se Won Suh b,d, ** a Department of Bio & Nano Chemistry, Kookmin University, Seoul 136-702, South Korea b Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, South Korea c Department of Chemistry, Mokpo National University, Mokpo 534-729, South Korea d Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, South Korea article info Article history: Received 24 July 2010 Available online 1 August 2010 Keywords: Pelota Dom34 eRF1 Structural plasticity No-go decay abstract Dom34 from Saccharomyces cerevisiae is one of the key players in no-go mRNA decay, a surveillance path- way by which an abnormal mRNA stalled during translation is degraded by an endonucleolytic cleavage. Its homologs called Pelota are found in other species. We showed previously that S. cerevisiae Dom34 (domain 1) has an endoribonuclease activity, which suggests its direct catalytic role in no-go decay. Pelota from Thermoplasma acidophilum and Dom34 from S. cerevisiae have been structurally character- ized, revealing a tripartite architecture with a significant difference in their overall conformations. To gain further insights into structural plasticity of the Pelota proteins, we have determined the crystal structures of two archaeal Pelotas from Archaeoglobus fulgidus and Sulfolobus solfataricus. Despite the structural similarity of their individual domains to those of T. acidophilum Pelota and S. cerevisiae Dom34, their overall conformations are distinct from those of T. acidophilum Pelota and S. cerevisiae Dom34. Different overall conformations are due to conformational flexibility of the two linker regions between domains 1 and 2 and between domains 2 and 3. The observed inter-domain structural plasticity of Pelota proteins suggests that large conformational changes are essential for their functions. Ó 2010 Elsevier Inc. All rights reserved. 1. Introduction A quality control system that recognizes defective mRNAs is an important aspect of gene expression. To protect cells from a harm- ful consequence of the abnormal mRNAs, mRNA quality control systems specifically recognize and degrade defective mRNAs [1]. At least three mRNA surveillance pathways are known. The most well characterized nonsense-mediated decay targets mRNAs with premature termination codons [2]. Nonstop decay degrades an abnormal mRNA that lacks termination codons [3,4]. The third sur- veillance pathway, termed no-go decay, was identified in Saccharo- myces cerevisiae [5]. Abnormal mRNAs that are stalled during translation were found to be endonucleolytically cleaved near the stall site and subsequently degraded [5,6]. Two S. cerevisiae pro- teins Dom34 (called Pelota in other species) and Hbs1 (H sp70 sub- family B suppressor 1) were identified to be required for the initial endoribonucleolytic cleavage [5]. We previously reported the tripartite structure of Pelota from Thermoplasma acidophilum (Ta) [7]. Its domain 1 has the RNA-bind- ing Sm fold, unlike domain 1 of eukaryotic release factor 1 (eRF1), while each of its domains 2 and 3 is structurally homologous with the corresponding domain of eRF1 [7]. Furthermore, we showed that S. cerevisiae Dom34 has an endoribonuclease activity against RNA substrates with a stable stem-loop and its domain 1 is suffi- cient for the catalytic activity [7]. Subsequently, the structure of S. cerevisiae Dom34 was reported [8]. Interestingly, the relative do- main orientations in S. cerevisiae Dom34 differed significantly from those of Ta Pelota despite the high structural similarity of individ- ual domains between S. cerevisiae Dom34 and Ta Pelota [8]. Three acidic residues Glu23, Glu26, and Asp27 of S. cerevisiae Dom34, which were shown to be important for the endoribonuclease activ- ity [7], are relatively less accessible to the solvent than the corre- sponding residues of Ta Pelota and thus it was suggested that a conformational change may occur to trigger the endonucleolytic cleavage [8]. To provide further structural data on inter-domain structural plasticity of Pelota proteins, we have determined crystal structures of two archaeal Pelotas from Archaeoglobus fulgidus (Af) and Sulfol- obus solfataricus (Sso). Af Pelota has sequence identities of 26% and 24% with Pelotas from human and S. cerevisiae, respectively, while Sso Pelota shows 23% identities. Remarkably, our crystal structures reveal that overall conformations of Af Pelota and Sso Pelota are not only different from each other but also distinct from those of Ta Pelota and S. cerevisiae Dom34. The conformational differences are essentially due to structural plasticity of the two linker regions 0006-291X/$ - see front matter Ó 2010 Elsevier Inc. All rights reserved. doi:10.1016/j.bbrc.2010.07.121 * Corresponding author. Address: Department of Bio & Nano Chemistry, Kookmin University, Seoul 136-702, South Korea. Fax: +82 2 910 4415. ** Corresponding author. Address: Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, South Korea. Fax: +82 2 889 1568. E-mail addresses: hhlee@kookmin.ac.kr (H.H. Lee), sewonsuh@snu.ac.kr (S.W. Suh). Biochemical and Biophysical Research Communications 399 (2010) 600–606 Contents lists available at ScienceDirect Biochemical and Biophysical Research Communications journal homepage: www.elsevier.com/locate/ybbrc