Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs

Eriani, Gilbert; Delarue, Marc; Poch, Olivier; Gangloff, Jean; Moras, Dino

doi:10.1038/347203a0

Cited by 1,361 publications

(1,154 citation statements)

References 28 publications

Supporting

Mentioning

1,109

Contrasting

Unclassified

Order By: Relevance

“…The specificity of a tRNA toward an amino acid (the tRNA identity) depends on the recognition of characteristic nucleotides (identity determinants) in the tRNA molecule by aaRS's [1][2][3][4][5][6]. Based on the sequences and the three-dimensional (3D) structures of the catalytic domains, the aaRS's are divided into two classes, each with ten synthetases [7]. In general, every class I synthetase has catalytic domains containing the classical nucleotide-binding (Rossmann) fold [8].…”

Section: Introduction 2 Materials and Methodsmentioning

confidence: 99%

A three‐dimensional structure model of the complex of glutamyl‐tRNA synthetase and its cognate tRNA

Tateno¹,

Nureki²,

Sekine³

et al. 1995

FEBS Letters

View full text Add to dashboard Cite

A docking model of glutamyl-tRNA synthetase (GIuRS) and tRNA Glu was constructed, on the basis of the distinguished similarity between the X-ray crystallographic three-dimensional structures of the N-terminal halves of the Thermus thermophilus GInRS in the free state and the Escherichia coli glutaminyl-tRNA synthetase in a complex with tRNA C~n. The modeled structure is energetically favorable and is also well consistent with the results of site-directed mutagenesis studies. The model indicates that the GluRS-specific insertions 2 and 3 fit and bind to the acceptor stem and the D arm, respectively, of the cognate tRNA without affecting other contacts. In particular, insertion 3 strongly interacts with the two D-stem base pairs that are essential for the tRNA'GIuRS recognition.

show abstract

Section: Introduction 2 Materials and Methodsmentioning

confidence: 99%

A three‐dimensional structure model of the complex of glutamyl‐tRNA synthetase and its cognate tRNA

Tateno¹,

Nureki²,

Sekine³

et al. 1995

FEBS Letters

View full text Add to dashboard Cite

show abstract

“…At this stage, it is instructive to observe that the 20 amino acids are divided into two classes of 10 each, according to the properties of their aminoacyl-tRNA synthetases (Eriani et al 1990, Arnez and Moras 1997, Lewin 2000. The two classes of synthetases totally differ from each other in their active sites and in how they attach amino acids to the tRNA molecules.…”

Section: Putting Things Togethermentioning

confidence: 99%

Carbon — the first frontier of information processing

Patel

2002

J Biosci

View full text Add to dashboard Cite

Information is often encoded as an aperiodic chain of building blocks.Modern digital computers use bits as the building blocks, but in general the choice of building blocks depends on the nature of the information to be encoded. What are the optimal building blocks to encode structural information? This can be analysed by substituting the operations of addition and multiplication of conventional arithmetic with translation and rotation.It is argued that at the molecular level, the best component for encoding discretised structural information is carbon. Living organisms discovered this billions of years ago, and used carbon as the back-bone for constructing proteins that function according to their structure. Structural analysis of polypeptide chains shows that an efficient and versatile structural language of 20 building blocks is needed to implement all the tasks carried out by proteins. Properties of amino acids indicate that the present triplet genetic code was preceded by a more primitive one, coding for 10 amino acids using two nucleotide bases.Keywords. Amino acid; aminoacyl-tRNA synthetase; computation; genetic code; information; lattice models; protein structure; quantum search; tetrahedral geometry Structural informationIt is a characteristic of living organisms to acquire information, interpret it and pass it on, often using it and refining it along the way. This information can be in various forms or languages. It can be genetic information passed on from the parent to the offspring, sensory information conveyed by the sense organ to the brain, linguistic information communicated by one being to another, or numerical data entered in a computer for later use. It is advantageous to process the information efficiently, and not in any haphazard manner. In case of living organisms, Darwinian selection during evolution can be considered the driving force for such optimisation. In general, information processing is optimised following two guidelines: minimisation of physical resources (time as well as space), and minimisation of errors.A striking feature of all the forms of information listed above is that the messages are represented as aperiodic chains of discrete building blocks. Such a representation, called digitisation of the message, is commonplace due to its many advantages. Discretisation makes it possible to correct errors arising from local disturbances, and so it is desirable even when the underlying physical variables are continuous (e.g. voltages and currents in computers). It is also easier to handle several variables each spanning a small range than a single variable covering a large range. Any desired message can then be constructed by putting together as many as necessary of the smaller range variables, while the instruction set required to manipulate each variable is substantially simplified. This simplification means that only a limited number of processes have to be physically implemented leading to high speed computation. An important question, therefore, is to figure out the best way...

show abstract

“…Lin (Eriani et al, 1990a) similar to HIGH for most of the class I aminoacyl-tRNA synthetases, the enzyme does not have sequence homologies with other aminoacyl-tRNA synthetases. Thus, another interesting characteristic relevant to structure-function study of ArgRS will be provided by its crystallization and subsequent structure determination.…”

mentioning

confidence: 92%

“…Arginyl-tRNA synthetase (ArgRS) is classified as a member of the class I aminoacyl-tRNA synthetases (aaRS) with specificity towards the 2'-OH of the tRNA terminal adenosine, based on the available structure-function information for aaRSs (Eriani et al, 1990a, Nureki et al, 1995. ArgRS has also been well known as a representative enzyme in a small group of aaRS with glutamyl-and glutaminyl-tRNA synthetases.…”

mentioning

confidence: 99%

Crystallization and preliminary X‐ray diffraction analysis of arginyl‐tRNA synthetase from Escherichia coli

et al. 1997

View full text Add to dashboard Cite

Arginyl-tRNA Synthetase, a class I aminoacyl tRNA synthetase playing a crucial role in protein biosynthesis, has been crystallized for the first time. Polyethylene glycol (PEG) was used as a precipitant, and the crystallization proceeded at pH 6.5. These single crystals diffracted to 2.8 8, with a rotating anode X-ray source and R-axis IIc image plate detector. They have an orthorhombic space group P2,2,2 with unit cell parameters of a = 251.51 8,. b = 53.12 8,, and c = 52.35 8,. A complete native data set has been collected at 3.1 A resolution for these crystals.Keywords: arginyl-tRNA synthetase; class I aminoacyl-tRNA synthetase; crystallization; protein biosynthesis; X-ray crystallography Aminoacyl-tRNA synthetases play a crucial role in protein biosynthesis. Arginyl-tRNA synthetase (ArgRS) is classified as a member of the class I aminoacyl-tRNA synthetases (aaRS) with specificity towards the 2'-OH of the tRNA terminal adenosine, based on the available structure-function information for aaRSs (Eriani et al., 1990a, Nureki et al., 1995. ArgRS has also been well known as a representative enzyme in a small group of aaRS with glutamyl-and glutaminyl-tRNA synthetases. In this small group the presence of tRNA is necessary for the ATP-PPi exchange reaction, in contrast to the majority of aminoacyl-tRNA synthetases (Ravel et al., 1964(Ravel et al., , 1965 Parfait & Grojean, 1972;Gangloff et al., 1976;Char & Gopinathan, 1986;Lin et al., 1988a Lin et al., , 1988b. The ATP-PPI exchange is usually an easy measurement of the amino acid activation for aaRSs.As the above three enzymes are also classified in the same subclass (IC) of aaRS with charged or polar amino acids as the substrate, structural information will permit a very interesting deReprints request to: Dr. s.-X. Lin tailed comparison of their structure-function relationships. The three-dimensional structures of glutaminyl-and glutamyl-tRNA synthetases have been determined with enzymes from E. coli and 7: thermophilus, respectively. Although ArgRS from E. coli. has a sequence of HVGH associated with a Rossmann fold (Eriani et al., 1990a) similar to HIGH for most of the class I aminoacyl-tRNA synthetases, the enzyme does not have sequence homologies with other aminoacyl-tRNA synthetases. Thus, another interesting characteristic relevant to structure-function study of ArgRS will be provided by its crystallization and subsequent structure determination. Here we report the crystallization and the preliminary crystallographic study of ArgRS.

show abstract

Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs

Cited by 1,361 publications

References 28 publications

A three‐dimensional structure model of the complex of glutamyl‐tRNA synthetase and its cognate tRNA

A three‐dimensional structure model of the complex of glutamyl‐tRNA synthetase and its cognate tRNA

Carbon — the first frontier of information processing

Crystallization and preliminary X‐ray diffraction analysis of arginyl‐tRNA synthetase from Escherichia coli

Contact Info

Product

Resources

About