Sarah Krautwurst

Friedrich Schiller University Jena | FSU · Department of Bioinformatics

The International Virus Bioinformatics Meeting 2022 took place online, on 23–25 March 2022, and has attracted about 380 participants from all over the world. The goal of the meeting was to provide a meaningful and interactive scientific environment to promote discussion and collaboration and to inspire and suggest new research directions and questi...

Storage and directed transfer of information is the key requirement for the development of life. Yet any information stored on our genes is useless without its correct interpretation. The genetic code defines the rule set to decode this information. Aminoacyl-tRNA synthetases are at the heart of this process. We extensively characterize how these e...

Genetic code and translation are key to all life. As a consequence, all kingdoms and species share the enzymes known as aminoacyl-tRNA synthetases, which link amino acids to their codons. For life to flourish, it is vital that these enzymes correctly implement the genetic code and hence correctly recognize amino acids. There are many theories on th...

The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significa...

Binding mode definition. Binding modes M1 and M2 are defined based on the complexed ligand: ligands that bind to the adenosine phosphate moiety (highlighted in red, only in contact when adenosine phosphate is part of the ligand) of the binding site (M1), no ligands or ligands that bind exclusively to the aminoacyl part (green) of the binding site (...

Core-interaction patterns. Both aaRS classes contain highly conserved patterns, responsible for proper binding of the adenosine phosphate part of the ligand. Class I aaRS share a highly conserved set of backbone hydrogen interactions with the ligand: the Backbone Brackets. Class II active sites contain a pattern of two arginine residues grasping th...

Origin organisms of aaRS Class I and Class II structures in the dataset. The organisms of origin for aaRS Class I (A) and Class II (B) structures in the dataset. The inner circles correspond to the superkingdom of the organism. The outer circle depicts the partition into specific species (combining different strains). Sections representing eukaryot...

Class II sequences in FASTA format. Protein sequences of Class II aaRS structures used to construct the structure-guided MSA in FASTA format. (FASTA)

Secondary structure of Backbone Brackets adjacent residues. WebLogo [75] representation of secondary structure elements around the Backbone Brackets residues (274 and 1361) annotated by DSSP [123]: helices (blues), strands (red), and unordered (black). Unassigned states are represented by the character “C”. The height of each character corresponds...

Dataset preparation. (DOCX)

Selection of representative entries. (DOCX)

Dataset as JSON file. Machine-readable JSON version of the dataset. Additionally enriched with protein sequence, sequence cluster identifier, and representative types for each dataset entry. (JSON)

Backbone Brackets failed mapping. List of structures where the mapping of the Backbone Brackets motif was not possible. (TXT)

Arginine Tweezers failed mapping. List of structures where the mapping of the Arginine Tweezers motif was not possible. (TXT)

Renumbering table for Class II structures. Formatted table that contains all sequence positions of the Class II MSA and annotations of sequence motifs, Arginine Tweezers residues, and ligand binding regions (rows). Each renumbered sequence position is related to its original sequence position for every structure in the dataset (columns). (XLSX)

Secondary structure of Arginine Tweezers adjacent residues. WebLogo [75] representation of secondary structure elements around the Arginine Tweezers residues (698 and 1786) annotated by DSSP [123]: helices (blues), strands (red), and unordered (black). Unassigned states are represented by the letter “C”. The height of each character corresponds to...

Distributions of alpha carbon distances for Backbone Brackets and Arginine Tweezers. Distributions of alpha carbon distances for Class I Backbone Brackets motif and Class II Arginine Tweezers motif in adenosine phosphate bound (M1) and unbound state (M2). The alpha carbon distance of the Backbone Brackets differs significantly between the two state...

Distributions of side chain angles for Backbone Brackets and Arginine Tweezers. Distributions of side chain angle θ for Class I Backbone Brackets motif and Class II Arginine Tweezers motif in adenosine phosphate bound (M1) and unbound state (M2). The side chain angles of the Arginine Tweezers differs differs significantly between the two states (Ma...

Alignments of Backbone Brackets and Arginine Tweezers. Structural backbone-only alignments of relevant binding site motifs computed with Fit3D [122]. Alignments are grouped by structures derived from adenosine phosphate bound (M1) and unbound state (M2) for aaRS Class I and Class II. (A,C) The Class I Backbone Brackets motif aligned in respect to M...

Pairwise sequence and structure similarity. Structure and sequence similarity for pairs of cluster representative chains for aaRS Class I (A) and II (B). Depicted is the sequence similarity (% identity) after a global Needleman-Wunsch [121] alignment of both structures against the structure similarity determined by TMAlign [73]. For Class I (Class...

Backbone RMSD of Backbone Brackets and Arginine Tweezers after superimposition. Averaged backbone RMSD values after all-vs-all superimposition are shown in this table. (DOCX)

Class I multiple sequence alignment. Structure-guided MSA of Class I sequences in FASTA format. (FASTA)

Class II multiple sequence alignment. Structure-guided MSA of Class II sequences in FASTA format. (FASTA)

Arginine Tweezers residue mapping. Mapping of the Arginine Tweezers Class II motif to sequence positions in origin structures. (TXT)

Renumbering table for Class I structures. Formatted table that contains all sequence positions of the Class I MSA and annotations of sequence motifs, Backbone Brackets residues, and ligand binding regions (rows). Each renumbered sequence position is related to its original sequence position for every structure in the dataset (columns). (XLSX)

Dataset as table. Summary table of all aaRS protein chains used for the analysis, including PDB identifier, chain identifier, superkingdom, taxonomy identifier, and ligand information (if any). (XLSX)

Class I sequences in FASTA format. Protein sequences of Class I aaRS structures used to construct the structure-guided MSA in FASTA format. (FASTA)

Backbone Brackets residue mapping. Mapping of the Backbone Brackets Class I motif to sequence positions in origin structures. (TXT)

Archive containing Class I renumbered structures. All structures of Class I aaRS with residues renumbered according to the MSA. (GZ)

The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significa...

Aminoacyl tRNA synthetases (aaRS) are key enzymes in protein biosynthesis. Understanding the complex interactions between aaRS and their ligands can help to shed light on an early phase in molecular evolution. Here we propose a workflow to annotate characteristic interaction patterns by combining two tools for the analysis of binding sites and func...