Gauss Dh

Compilation of tRNA sequences

This compilation presents in a small space the tRNA sequences so far published in order to enable rapid orientation and comparison. The numbering of tRNAPhe from yeast is used as has been done earlier (1) but following the rules proposed by the participants of the Cold Spring Harbor Meeting on tRNA 1978 (2) (Fig. 1). This numbering allows comparisons with the three dimensional structure of tRNAPhe, the only structure known from X-ray analysis. The secondary structure of tRNAs is indicated by specific underlining. In the primary structure a nucleoside followed by a nucleoside in brackets or a modification in brackets denotes that both types of nucleosides can occupy this position. Part of a sequence in brackets designates a piece of sequence not unambiguously analyzed. Rare nucleosides are named according to the IUPAC-IUB rules (for some more complicated rare nucleosides and their identification see Table 1); those with lengthy names are given with the prefix x and specified in the footnotes. Footnotes are numbered according to the coordinates of the corresponding nucleoside and are indicated in the sequence by an asterisk. The references are restricted to the citation of the latest publication in those cases where several papers deal with one sequence. For additional information the reader is referred either to the original literature or to other tRNA sequence compilations (3--7). Mutant tRNAs are dealt with in a separate compilation prepared by J. Celis (see below). The compilers would welcome any information by the readers regarding missing material or erroneous presentation. On the basis of this numbering system computer printed compilations of tRNA sequences in a linear form and in cloverleaf form are in preparation.

ATP binding site of P2X channel proteins: structural similarities with class II aminoacyl-tRNA synthetases.

The extracellular loop of P2X channel proteins contains a sequence stretch (positions 170–330) that exhibits similarities with the catalytic domains of class II aminoacyl‐tRNA synthetases as shown by secondary structure predictions and sequence alignments. The arrangement of several conserved cysteines (positions 110–170) shows similarities with metal binding regions of metallothioneins and zinc finger motifs. Thus, for the extracellular part of P2X channel proteins a metal binding domain and an antiparallel six‐stranded β‐pleated sheet containing the ATP binding site are very probable. The putative channel forming H5 part (positions 320–340) shows similarities with the enzyme motif 1 responsible for aggregation of subunits to the holoenzyme.

Histidyl-tRNA synthetase.

Abstract Histidyl-tRNA synthetase (HisRS) is responsible for the synthesis of histidyl-transfer RNA, which is essential for the incorporation of histidine into proteins. This amino acid has uniquely moderate basic properties and is an important group in many catalytic functions of enzymes. A compilation of currently known primary structures of HisRS shows that the subunits of these homodimeric enzymes consist of 420–550 amino acid residues. This represents a relatively short chain length among aminoacyl-tRNA synthetases (aaRS), whose peptide chain sizes range from about 300 to 1100 amino acid residues. The crystal structures of HisRS from two organisms and their complexes with histidine, histidyl-adenylate and histidinol with ATP have been solved. HisRS from Escherichia coli and Thermus thermophilus are very similar dimeric enzymes consisting of three domains: the N-terminal catalytic domain containing the sixstranded antiparallel β-sheet and the three motifs characteristic of class II aaRS, a HisRS-specific helical domain inserted between motifs 2 and 3 that may contact the acceptor stem of the tRNA, and a C-terminal α/β domain that may be involved in the recognition of the anticodon stem and loop of tRNAHis. The aminoacylation reaction follows the standard two-step mechanism. HisRS also belongs to the group of aaRS that can rapidly synthesize diadenosine tetraphosphate, a compound that is suspected to be involved in several regulatory mechanisms of cell metabolism. Many analogs of histidine have been tested for their properties as substrates or inhibitors of HisRS, leading to the elucidation of structure-activity relationships concerning configuration, importance of the carboxy and amino group, and the nature of the side chain. HisRS has been found to act as a particularly important antigen in autoimmune diseases such as rheumatic arthritis or myositis. Successful attempts have been made to identify epitopes responsible for the complexation with such auto-antibodies.

Formation of cyclodextrin inclusion compounds of stable nitroxide radicals as monitored by electron-spin resonance spectra

Abstract Hyperfine coupling constants and rotational correlation times, calculated from electron-spin resonance spectra of cyclodextrins incubated with stable nitroxide radicals, indicate inclusion compound formation of β- and γ-cyclodextrin with certain nitroxide radicals. In contrast, α-cycledextrin exhibits no effect on the spectra of the radicals, probably because its central cavity is too small to form such inclusion compounds. Furthermore, one 1:1 molar ratio complex of β-cyclodextrin and a nitroxide radical (isolated as crystalline precipitate and identified both by combustion analysis and ir measurements) is shown by electron-spin resonance data to be an inclusion compound.

APPENDIX I: Proposed Numbering System of Nucleotides in tRNAs Based on Yeast tRNA Phe

This compilation presents in a small space the tRNA sequences so far published to enable rapid orientation and comparison. The numbering of tRNA phe from yeast is used as has been done earlier1 but following the rules proposed by the participants of the 1978 Cold Spring Harbor Meeting on tRNA. This numbering allows comparisons with the three-dimensional structure of tRNA phe , the only structure known from X-ray analysis. The secondary structure of tRNAs is indicated by specific underlining. In the primary structure, a nucleoside followed by a nucleoside in brackets or a modification in brackets denotes that both types of nucleosides can occupy this position. Part of a sequence in brackets designates a piece of sequence not unambiguously analyzed. Rare nucleosides are named according to the IUPAC-IUB rules (for some, more complicated, rare nucleosides and their identification, see Table 1); those with lengthy names are given with the prefix “x” and specified in the footnotes. Footnotes are numbered according to the coordinates of the corresponding nucleoside and are indicated in the sequence by an asterisk. The references are restricted to the citation of the latest publication in those cases where several papers deal with one sequence. For additional information, refer either to the original literature or to other tRNA sequence compilations.2–6 Table Table 1Names of some rare nucleosides and citations regarding their identification NucleosideIdentificationo 5 Uuridine-5-oxyacetic acidmo 5 U5-methoxyuridinemcm 5 U5-methoxycarbonylmethyluridine 1 mcm 5 s 2 U5-methoxycarbonylmethyl-2-thiouridinemam 5 s 2 U5- N- methylaminomethyl-2-thiouridinei 6 A N -6-(Δ 2 -isopentenyl)adenosinems 2 i 6 A N -6-(Δ 2 -isopentenyl)2-methylthioadenosine 3 t 6 A N -[9-( β -D-ribofuranosyl)purin-6-ylcarbamoyl]threoninemt 6 A N -[9-( β -D-ribofuranosyl)purin-6-yl- N -methylcarbamoyl]threonineQ 34 7-(4,5- cis dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanosine 4 X3- N -(3-amino-3-carboxypropyl)uridine 5 y W wybutosine 6 O 2 yW