Crystal structure of human Acinus RNA recognition motif domain.

Humberto Fernandes,Honorata Czapinska,Katarzyna Grudziaz,Martyna Nowacka,Janusz M. Bujnicki

doi:10.7717/peerj.5163

Abstract

Acinus is an abundant nuclear protein involved in apoptosis and splicing. It has been implicated in inducing apoptotic chromatin condensation and DNA fragmentation during programmed cell death. Acinus undergoes activation by proteolytic cleavage that produces a truncated p17 form that comprises only the RNA recognition motif (RRM) domain. We have determined the crystal structure of the human Acinus RRM domain (AcRRM) at 1.65 Å resolution. It shows a classical four-stranded antiparallel β-sheet fold with two flanking α-helices and an additional, non-classical α-helix at the C-terminus, which harbors the caspase-3 target sequence that is cleaved during Acinus activation. In the structure, the C-terminal α-helix partially occludes the potential ligand binding surface of the β-sheet and hypothetically shields it from non-sequence specific interactions with RNA. Based on the comparison with other RRM-RNA complex structures, it is likely that the C-terminal α-helix changes its conformation with respect to the RRM core in order to enable RNA binding by Acinus.

Highlights

The RNA recognition motif (RRM) is a small protein domain known for its characteristic babbab fold and frequent engagement in RNA binding
The two Acinus RRM domain (AcRRM) monomers are covalently bound in the crystal structure via a disulfide bond (Fig. 2B), that generates an interface area of approximately 500 Afor each of them (calculated by the PISA server (Krissinel, 2015))
The monomeric state of AcRRM in reducing conditions was confirmed by gel domain. (A) Overview of the human AcRRM domain colored according to the position in the sequence (RNP1 and RNP2 are located in the green and blue colored b-strands, the C-terminal a-helix is colored in red). (B) Amino acid sequence conservation of AcRRM calculated using the ConSurf server (Ashkenazy et al, 2010) and mapped on the solvent excluded surface of the protein. (C) The electrostatic potential of AcRRM calculated using the DelPhi server (Li et al, 2012) and mapped on the solvent accessible surface of the domain

Summary

Introduction

The RNA recognition motif (RRM) is a small (approximately 90 residues) protein domain known for its characteristic babbab fold and frequent engagement in RNA binding. Binding involves two conserved motifs termed RNP1 and RNP2, located in the two central b-strands, with [RK]-G-[FY]-[GA]-[FY][ILV]-X-[FY] and [ILV]-[FY]-[ILV]-X-N-L consensus sequences, respectively (X stands for any amino acid) (Maris, Dominguez & Allain, 2005; Clery, Blatter & Allain, 2008). Prominent features of these motifs include conserved aromatic residues that are often involved in interactions with ribonucleotides of the RNA target sequence.

Methods

Results

Discussion

Conclusion