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Topic: TRNA

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	Transfer RNA - Wikipedia, the free encyclopedia
		Transfer RNA (abbreviated tRNA) is a small RNA chain (74-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation.
		The codon recognition is different for each tRNA and is determined by the anticodon region, which contains the complementary bases to the ones encountered on the mRNA.
		Recognition of the approriate tRNA by the synthetases in not mediated solely by the anticodon, and the acceptor stem often plays a prominent role.
	en.wikipedia.org /wiki/TRNA (726 words)

	Exercise 8. tRNA
		The region of the tRNA molecule that interacts with the messenger is known as the anticodon.
		To reduce the number of tRNAs necessary to read the codons, the wobble position is often intended to base pair with two or three different bases at the 3' end of the codon.
		It appears that one approach taken by nature to enhance the specific base pairing interactions between tRNA and mRNA is to use modified bases at positions flanking the anticodon in the tRNA molecule.
	www.cgl.ucsf.edu /home/glasfeld/tutorial/trna/trna.html (1422 words)

	PDB Molecule of the Month: Aminoacyl-tRNA Synthetases
		These enzymes charge each tRNA with the proper amino acid, thus allowing each tRNA to make the proper translation from the genetic code of DNA into the amino acid code of proteins.
		The one shown here, which charges aspartic acid onto the proper tRNA (entry 1asz), is a dimer of two identical subunits (colored blue and green, the two tRNA molecules are colored red).
		So, tRNA molecules are also recognized using segments on the acceptor end and bases elsewhere in the molecule.
	www.rcsb.org /pdb/molecules/pdb16_1.html (519 words)

	Compilation of tRNA sequences and sequences of tRNA genes
		All the information collected is split into different indexed tables according to the type of data (specificity, sequence, organism, etc.) and the descriptions of certain genes are summarised in the main worksheet that includes the relations between the data tables.
		Terminology and structure of the modified nucleosides occurring in tRNAs were used according to (5) and (6).
		Each sequence in the Compilation of tRNA Sequences and Compilation of tRNA Genes has unique six-position identification code of the sequence ('D' or 'R' for DNA or RNA, respectively; a one-letter code for the amino acid, X for methionine-initiator, Z for selenocysteine; the three-digit code specifying the organism and one digit for isoacceptor number).
	www.uni-bayreuth.de /departments/biochemie/trna (1010 words)

	Pus1p-dependent tRNA Pseudouridinylation Becomes Essential When tRNA Biogenesis Is Compromised in Yeast -- ...
		In vitro transcribed tRNAs were incubated with the extracts for 30 min at 30 °C; numbers correspond to mole of the examined modification per mole of tRNA.
		this tRNA was a substrate of the pseudouridine synthase Pus1p,
		Arrows (in the case of nuclear tRNA accumulation) or arrowheads (lack of accumulation) point to the nucleoplasmic space in representative cells as judged by DAPI staining of DNA.
	www.jbc.org /cgi/content/full/276/49/46333 (4776 words)

	Transcription and Translation (Site not responding. Last check: 2007-11-07)
		Most tRNA molecules are about 76 nucleotides in length, but they range from 60 to 95.
		The tRNA molecules fold into a cloverleaf secondary structure that is held in shape by base pairing in at least four regions.
		The anticodon is on a loop at the opposite end of the molecule to the amino acid binding region.
	www.brooklyn.cuny.edu /bc/ahp/BioInfo/TT/Tlatt.html (207 words)

	tRNA transfers to the limelight -- Hopper and Phizicky 17 (2): 162 -- Genes and Development
		A schematic of a tRNA precursor and a mature tRNA.
		It is unclear whether tRNA aminoacylation is important for this pathway, and it is therefore indicated by a question mark.
		A major tRNA nuclear egress route for yeast is known to exist, and aminoacylation and Cca1p participate in this mechanism, but the details of their actions are not known and are indicated by question marks.
	www.genesdev.org /cgi/content/full/17/2/162 (8001 words)

	tRNA Synthetase (Site not responding. Last check: 2007-11-07)
		Individual tRNA's contain a recognition element (the anticodon loop) which recognises the complementary triplet of bases on the m-RNA encoding for the amino acid in the protein, so ensuring incorporation of the correct amino acid.
		Crystal structures of tyrosyl tRNA synthetase from Bacillus stearothermophilus have been solved for the enzyme itself, the enzyme complexed to tyrosine and to tyrosyl-adenylate intermediate and for several mutants [2-6].
		However, even when modelled in their extended conformations the side chain amino functions cannot be located closer than 8 angstroms from the phosphates of ATP in the transition state, suggesting that the loop containing these residues must move to wrap around the transition state in an induced fit mechanism.
	www.cryst.bbk.ac.uk /pps97/assignments/projects/irving/project.htm (3338 words)

	Visualization of tRNA Movements on the Escherichia coli 70S Ribosome During the Elongation Cycle -- Agrawal et al. 150 ...
		The PRE complex also shows an unexpected mass corresponding to the E-site tRNA on the L1 protein side, which is due to the binding of deacylated tRNA in a fraction of PRE complex.
		of the P-site tRNA (Fig 2, Fig 5 b, and 7 a).
		The tRNA portion of the unbound ternary complex is presented in gray, the EF-Tu portion in red.
	www.jcb.org /cgi/content/full/150/3/447 (7488 words)

	5' end maturation and RNA editing have to precede tRNA 3' processing in plant mitochondria -- Kunzmann et al. 95 (1): ...
		A special feature of mitochondrial tRNA maturation in plant cells is the involvement of RNA editing (18-20).
		tRNAs are imported as precursor molecules or as mature tRNAs.
		being that tRNAs are not excised from unedited precursors.
	www.pnas.org /cgi/content/full/95/1/108 (4324 words)

	Single amino acid changes in AspRS reveal alternative routes for expanding its tRNA repertoire in vivo -- Martin et al. ...
		the tRNA to the OB-fold is nearly the same (31,33,42–44).
		Salazar,J., Ivan Ahel,I., Orellana,O., Tumbula-Hansen,D., Krieger,R., Daniels,L. and Söll,D. ((2003)) Coevolution of an aminoacyl-tRNA synthetase with its tRNA substrates.
		Kisselev,L. ((1985)) The role of the anticodon in recognition of tRNA by aminoacyl-tRNA synthetases.
	nar.oupjournals.org /cgi/content/full/32/13/4081 (5216 words)

	Physiological analysis of the role of truB in Escherichia coli: a role for tRNA modification in extreme temperature ...
		Physiological analysis of the role of truB in Escherichia coli: a role for tRNA modification in extreme temperature resistance -- Kinghorn et al.
		Buck, M. and Griffiths, E. Iron mediated methylation of tRNA as a regulator of operon expression in Escherichia coli.
		Persson, B. C., Gustafsson, C., Berg, D. and Björk, G. The gene for a tRNA modifying enzyme, m5U54-methyltransferase, is essential for viability in Escherichia coli.
	mic.sgmjournals.org /cgi/content/full/148/11/3511 (5413 words)

	Pfam 18.0 : tRNA-synt_2b (Site not responding. Last check: 2007-11-07)
		This domain is the core catalytic domain of tRNA synthetases and includes glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases.
		In reactions catalysed by the class I aminoacyl-tRNA synthetases,the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred.
		Class-II tRNA synthetases do not share a high degree of similarity, however at least three conserved regions are present MEDLINE:8274143, MEDLINE:2053131, MEDLINE:1852601.
	pfam.wustl.edu /cgi-bin/getdesc?acc=PF00587 (357 words)

	Location alters tRNA identity: Trypanosoma brucei's cytosolic elongator tRNAMet is both the initiator and elongator in ...
		Location alters tRNA identity: Trypanosoma brucei's cytosolic elongator tRNAMet is both the initiator and elongator in mitochondria -- Martin 99 (3): 1110 -- Proceedings of the National Academy of Sciences
		tRNA is thought to serve for both initiation and elongation (3).
		tRNAs can be made to function in both elongation and initiation regardless of whether their wild-type counterparts normally function in one role or the other.
	www.pnas.org /cgi/content/full/99/3/1110 (1759 words)

	Improvement of reading frame maintenance is a common function for several tRNA modifications
		After a normal three nucleotide translocation, the near-cognate tRNA slips into either -1 or +1 frame, depending on the sequence of the mRNA.
		(C) As in (A), but the hypomodified cognate tRNA is accepted in the A-site, and after a normal three nucleotide translocation to the P-site, the hypo modification induces slippage into the -1 or +1 frame.
		For clarity, only one tRNA is depicted as residing on the ribosome, although two tRNAs are always present in the A- and P-sites or P- and E-sites.
	www.nature.com /emboj/journal/v20/n17/fig_tab/7593982ft.html (730 words)

	tRNA & Ribosomes
		Minimally 31 tRNAs are required for translation, not counting the tRNA that codes for chain initiation.
		They bind to opposite sides of the tRNA acceptor stem, resulting in aminoacylation of a different hydroxyl of the tRNA.
		At right is a cut-away view showing the position of messenger RNA (schematically represented as orange beads), as well as P- and E-site tRNAs (based on x-ray structures, shown in green and yellow).
	www.rpi.edu /dept/bcbp/molbiochem/MBWeb/mb2/part1/trna.htm (1595 words)

	tRNAscan-SE Search Server (Site not responding. Last check: 2007-11-07)
		: The tRNA View function is currently not working because have retired some old equipment.
		We will try to have up and running again some time this summer (this notice will be updated when it is fixed).
		The Lowe lab at UCSC also hosts a tRNAscan-SE server as well as a Genomic tRNA Database of completed genomes analyzed with tRNAscan-SE.
	www.genetics.wustl.edu /eddy/tRNAscan-SE (130 words)

	Role of Nuclear Pools of Aminoacyl-tRNA Synthetases in tRNA Nuclear Export -- Azad et al. 12 (5): 1381 -- Molecular ...
		for tRNA probes and 37°C for the poly(A) RNA probe (10 min/wash).
		To determine the consequences of the NLS mutations on the catalytic activity of Tys1p we assessed enzyme activity in vitro.
		(B) tRNA aminoacylation in the nucleus and Los1p act in parallel in two tRNA nuclear export pathways, and there are other important export pathways yet to be identified.
	www.molbiolcell.org /cgi/content/full/12/5/1381 (7016 words)

	Three Modifications in the D and T Arms of tRNA Influence Translation in Escherichia coli and Expression of Virulence ...
		Three Modifications in the D and T Arms of tRNA Influence Translation in Escherichia coli and Expression of Virulence Genes in Shigella flexneri -- Urbonavicius et al.
		Three Modifications in the D and T Arms of tRNA Influence Translation in Escherichia coli and Expression of Virulence Genes in Shigella flexneri
		Pan, H., Agarwalla, S., Moustakas, D. T., Finer-Moore, J., Stroud, R. Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit.
	jb.asm.org /cgi/content/abstract/184/19/5348 (433 words)

	Aminoacyl-tRNA synthetase complexes: beyond translation -- Lee et al. 117 (17): 3725 -- Journal of Cell Science
		A schematic hypothetical model for the organization of mammalian, yeast and archea tRNA synthetase complexes.
		A cofactor of tRNA synthetase, p43, is secreted to up-regulate proinflammatory genes.
		Mucha, P. Aminoacyl-tRNA synthetases and aminoacylation of tRNA in the nucleus.
	jcs.biologists.org /cgi/content/full/117/17/3725 (6933 words)

	PDB Molecule of the Month: Transfer RNA
		Instead, the match is made by transfer RNA, the Rosetta Stone that translates the nucleotide language of codons into the amino acid language of proteins.
		This translation is physical and direct: at one end of each tRNA is an anticodon that recognizes the genetic code, and at the other end is the appropriate amino acid for that code.
		A battery of enzymes, termed amino-acyl tRNA synthases, are in charge of this job.
	www.rcsb.org /pdb/molecules/pdb15_1.html (513 words)

	The renaissance of aminoacyl-tRNA synthesis -- Ibba and Söll 2 (5): 382 -- EMBO Reports (Site not responding. Last check: 2007-11-07)
		An uncharged tRNA and the corresponding amino acid are first selected from the cellular pools of similar molecules by the appropriate AARS (see text for details).
		Lund, E. and Dahlberg, J.E. (1998) Proofreading and aminoacylation of tRNAs before export from the nucleus.
		Rho, S.B. and Martinis, S.A. (2000) The bI4 group I intron binds directly to both its protein splicing partners, a tRNA synthetase and maturase, to facilitate RNA splicing activity.
	emboreports.npgjournals.com /cgi/content/full/2/5/382 (3804 words)

	DNA - Wikipedia, the free encyclopedia
		Some genes code for "RNA genes" (see tRNA and rRNA).
		Some RNA genes code for transcripts that function as regulatory RNAs (see siRNA) that influence the function of other RNA molecules.
		This page was last modified 02:07, 22 October 2005.
	en.wikipedia.org /wiki/DNA (5200 words)

	In Vitro Import of a Nuclearly Encoded tRNA into Mitochondria of Solanum tuberosum -- Delage et al. 23 (11): 4000 -- ...
		In Vitro Import of a Nuclearly Encoded tRNA into Mitochondria of Solanum tuberosum -- Delage et al.
		Some of the mitochondrial tRNAs of higher plants are nuclearly
		Goswami, S., Chatterjee, S., Bhattacharyya, S. N., Basu, S., Adhya, S. Allosteric regulation of tRNA import: interactions between tRNA domains at the inner membrane of Leishmania mitochondria.
	mcb.asm.org /cgi/content/abstract/23/11/4000 (371 words)

	IMB Jena Image Library: Index of RNA structures
		MODEL - THE INTERACTION BETWEEN MRNA AND TRNA (MODEL A) 1q5s THEORET.
		MODEL - THE INTERACTION BETWEEN MRNA AND TRNA (MODEL D) 1r4h NMR - NMR SOLUTION STRUCTURE OF THE IIIC DOMAIN OF GB VIRUS B IRES ELEMENT 1r7p THEORET.
		MODEL - THE INTERACTION BETWEEN MRNA AND TRNA (MODEL A2) 1rd0 THEORET.
	www.imb-jena.de /IMAGE_RNA.html (773 words)

	On the Evolution of Structure in Aminoacyl-tRNA Synthetases -- O'Donoghue and Luthey-Schulten 67 (4): 550 -- ...
		Conservation of contacts between the AARS catalytic domain and the amino acid substrate, AMP, tRNA-CCA acceptor trinucleotide, and the rest of the tRNA.
		Aminoacyl-adenylate binding contacts are well conserved already at the class level, while the tRNA contacts are only partially present.
		The specific residues in the PDB files corresponding to the indices are given in the supplementary material.
	mmbr.asm.org /cgi/content/full/67/4/550 (9747 words)

	Taylor Ranch Neighborhood Association (TRNA) - Community
		This part of our web site is intended to help our residents communicate and learn more about Taylor Ranch and the surrounding area.
		TRNA Forum is a virtual location were we can communicate about issues important to Taylor Ranch residents and let each other know about events, issues, and questions.
		Learn about our community through the events held by TRNA and in Taylor Ranch.
	trna.org /community.html (148 words)

	Role of a 300-Kilodalton Nuclear Complex in the Maturation of Trypanosoma brucei Initiator Methionyl-tRNA -- Arhin et ...
		tRNAs are transcribed as precursors containing 5' leader and
		of tRNAs in parasitic protozoa and suggest that at least for
		Mailing address: Department of Epidemiology and Public Health, Yale University Medical School, 295 Congress Ave., New Haven, CT 06536-0812.
	ec.asm.org /cgi/content/abstract/3/4/893 (274 words)

	Pus1p-dependent tRNA Pseudouridinylation Becomes Essential When tRNA Biogenesis Is Compromised in Yeast -- ...
		Division of Labor Among the Yeast Sol Proteins Implicated in tRNA Nuclear Export and Carbohydrate Metabolism
		Utp8p Is an Essential Intranuclear Component of the Nuclear tRNA Export Machinery of Saccharomyces cerevisiae
		J. MALIK, and E. Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9
	www.jbc.org /cgi/content/abstract/276/49/46333 (525 words)

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