Crystal Structure of Human Mitochondrial PheRS Complexed with tRNAPhe in the Active “Open” State

Klipcan, Liron; Moor, Nina; Finarov, Igal; Kessler, Naama; Sukhanova, Maria V.; Safro, Mark

doi:10.1016/j.jmb.2011.11.029

Cited by 42 publications

(75 citation statements)

References 45 publications

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“…45 ), the homology-model of the HsaCCA and the crystal structure of the yeast tRNA for phenylalanine (see ref. 46 ) were energy-minimized with YASARA (see ref. 27 ) and joined in a search space cuboid with an edge length of 10.0 nm.…”

Section: Macromolecular Docking Simulationmentioning

confidence: 99%

Domain movements during CCA-addition: A new function for motif C in the catalytic core of the human tRNA nucleotidyltransferases

Ernst¹,

Rickert

Bluschke³

et al. 2015

RNA Biology

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These authors equally contributed to this work.Keywords: CCA-adding enzyme, CCA-addition, DEER, EPR spectroscopy, tRNA nucleotidyltransferase, tRNA, tRNA maturation CCA-adding enzymes are highly specific RNA polymerases that synthesize and maintain the sequence CCA at the tRNA 3 0 -end. This nucleotide triplet is a prerequisite for tRNAs to be aminoacylated and to participate in protein biosynthesis. During CCA-addition, a set of highly conserved motifs in the catalytic core of these enzymes is responsible for accurate sequential nucleotide incorporation. In the nucleotide binding pocket, three amino acid residues form Watson-Crick-like base pairs to the incoming CTP and ATP. A reorientation of these templating amino acids switches the enzyme's specificity from CTP to ATP recognition. However, the mechanism underlying this essential structural rearrangement is not understood. Here, we show that motif C, whose actual function has not been identified yet, contributes to the switch in nucleotide specificity during polymerization. Biochemical characterization as well as EPR spectroscopy measurements of the human enzyme reveal that mutating the highly conserved amino acid position D139 in this motif interferes with AMP incorporation and affects interdomain movements in the enzyme. We propose a model of action, where motif C forms a flexible spring element modulating the relative orientation of the enzyme's head and body domains to accommodate the growing 3 0 -end of the tRNA. Furthermore, these conformational transitions initiate the rearranging of the templating amino acids to switch the specificity of the nucleotide binding pocket from CTP to ATP during CCA-synthesis.

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Section: Macromolecular Docking Simulationmentioning

confidence: 99%

Domain movements during CCA-addition: A new function for motif C in the catalytic core of the human tRNA nucleotidyltransferases

Ernst¹,

Rickert

Bluschke³

et al. 2015

RNA Biology

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“…An example of a slide prepared by a student to identify particular residues in the assigned structure is shown in Fig. 1 Lassa virus NP-RNA Crystal structure of the Lassa virus nucleoprotein-RNA complex reveals a gating mechanism for RNA binding [24] hmPheRS-tRNA phe Crystal structure of human mitochondrial PheRS complexed with tRNA(Phe) in the active "open" state [25] FoxM1-DNA Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence [26] REX-DNA Structural basis for NADH/NAD1 redox sensing by a Rex family repressor [27] Together, these activities require students to apply a variety of software methods to specific structural problems, and to observe relationships between evolutionary conservation of residues and the structural and functional roles of those residues in the structure. Once they leave this guided and structured session, the students are charged with developing a presentation of the structure(s) described in their paper.…”

Section: Capstonementioning

confidence: 99%

Teaching structure: Student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course

Jaswal

O’Hara

Williamson

et al. 2013

Biochem Molecular Bio Educ

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Because understanding the structure of biological macromolecules is critical to understanding their function, students of biochemistry should become familiar not only with viewing, but also with generating and manipulating structural representations. We report a strategy from a one-semester undergraduate biochemistry course to integrate use of structural representation tools into both laboratory and homework activities. First, early in the course we introduce the use of readily available open-source software for visualizing protein structure, coincident with modules on amino acid and peptide bond properties. Second, we use these same software tools in lectures and incorporate images and other structure representations in homework tasks. Third, we require a capstone project in which teams of students examine a protein-nucleic acid complex and then use the software tools to illustrate for their classmates the salient features of the structure, relating how the structure helps explain biological function. To ensure engagement with a range of software and database features, we generated a detailed template file that can be used to explore any structure, and that guides students through specific applications of many of the software tools.In presentations, students demonstrate that they are successfully interpreting structural information, and using representations to illustrate particular points relevant to function. Thus, over the semester students integrate information about structural features of biological macromolecules into the larger discussion of the chemical basis of function. Together these assignments provide an accessible introduction to structural representation tools, allowing students to add these methods to their biochemical toolboxes early in their scientific development. V C 2013 by The

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“…The three other mt-aaRSs display a more electropositive tRNA-binding interface, which may favor interactions with the sugar-phosphate backbone of the substrate to compensate for a reduction of specific contacts with identity elements (Neuenfeldt et al 2013). The ability of mt-TyrRS, mt-PheRS, and mt-AspRS to aminoacylate heterologuous tRNAs (Bonnefond et al 2005a;Klipcan et al 2012;Neuenfeldt et al 2013) indicates a much higher substrate tolerance, which may be linked to an increased structural plasticity. For instance, mt-PheRS undergoes a large movement of its anticodonbinding domain upon tRNA binding, switching from a closed to an open conformation (Klipcan et al 2012).…”

Section: Crystallographic Structuresmentioning

confidence: 99%

Translation in Mammalian Mitochondria: Order and Disorder Linked to tRNAs and Aminoacyl-tRNA Synthetases

Florentz

Pütz

Jühling

et al. 2013

Translation in Mitochondria and Other Organelles

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Transfer RNAs (tRNAs) and aminoacyl-tRNA synthetases (aaRSs) are key actors in all translation machineries. AaRSs aminoacylate cognate tRNAs with a specific amino acid that is transferred to the growing protein chain on the ribosome. Mammalian mitochondria possess their own translation machinery for the synthesis of 13 proteins only, all subunits of the respiratory chain complexes involved in the synthesis of ATP. While 22 tRNAs and two ribosomal RNAs are also coded by the mitochondrial genome, aaRSs are nuclear encoded and become imported. The fact that the two cellular genomes, nuclear and mitochondrial,

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Crystal Structure of Human Mitochondrial PheRS Complexed with tRNAPhe in the Active “Open” State

Cited by 42 publications

References 45 publications

Domain movements during CCA-addition: A new function for motif C in the catalytic core of the human tRNA nucleotidyltransferases

Domain movements during CCA-addition: A new function for motif C in the catalytic core of the human tRNA nucleotidyltransferases

Teaching structure: Student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course

Translation in Mammalian Mitochondria: Order and Disorder Linked to tRNAs and Aminoacyl-tRNA Synthetases

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