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PMID: 10872325 Published · ppublish English Journal Article

A model for the tertiary structure of mammalian mitochondrial transfer RNAs lacking the entire 'dihydrouridine' loop and stem.

The EMBO journal ·Vol. 2 ·No. 8 ·1983-00-00 ·Pages 1309-21

de Bruijn MH, Klug A

Abstract

The mammalian mitochondrial tRNA(AGY)Ser is unique in lacking the entire dihydrouridine arm. This reduces its secondary structure to a 'truncated cloverleaf'. Experimental evidence on the tertiary structure has been obtained by chemically probing the conformation of both the bovine and human species in their native conformation and at various stages of denaturation. A structural model of the bovine tRNA is presented based on the results of this chemical probing, on a comparison between nine homologous 'truncated cloverleaf' secondary structures and on analogies with the crystal structure of yeast phenylalanine tRNA. The proposed structure is very similar in shape to that of yeast tRNA(Phe) but is slightly smaller in size. It is defined by a unique set of tertiary interactions. Structural considerations suggest that other mammalian mitochondrial tRNAs have smaller dimensions as well.

MeSH Terms
Animals Base Sequence Cattle Humans Mitochondria Models, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry RNA, Mitochondrial RNA, Transfer, Phe/chemistry RNA, Transfer, Ser/chemistry Solutions Uridine
Chemicals
RNA, Mitochondrial RNA, Transfer, Phe RNA, Transfer, Ser Solutions RNA Uridine
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
de Bruijn M H
Laboratory of Molecular Biology, Medical Research Council Centre, Cambridge, UK.
Klug A
References (37)
37 references, click to expand
  1. Correlation between three-dimensional structure and chemical reactivity of transfer RNA.
    Nucleic Acids Res. 1974 Jul;1(7):927-32 PMID: 10793725
  2. A simplified procedure for the preparation of tyrosine and valine-acceptor fractions of yeast "soluble ribonucleic acid".
    J Biol Chem. 1961 Jan;236:200-2 PMID: 13715347
  3. Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams.
    Biochemistry. 1972 Nov 7;11(23):4358-68 PMID: 4562590
  4. UV shadowing--a new and convenient method for the location of ultraviolet-absorbing species in polyacrylamide gels.
    Anal Biochem. 1974 May;59(1):162-4 PMID: 4407732
  5. Structure of yeast phenylalanine tRNA at 3 A resolution.
    Nature. 1974 Aug 16;250(467):546-51 PMID: 4602655
  6. Conformational changes of transfer ribonucleic acid. The pH phase diagram under acidic conditions.
    Biochemistry. 1974 Jun 18;13(13):2771-5 PMID: 4603218
  7. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA.
    J Mol Biol. 1974 Jul 25;87(1):63-88 PMID: 4610153
  8. The structural geometry of co-ordinated base changes in transfer RNA.
    J Mol Biol. 1974 Nov 5;89(3):511-6 PMID: 4613865
  9. Structural and energetic consequences of noncomplementary base oppositions in nucleic acid helices.
    Prog Nucleic Acid Res Mol Biol. 1975;15(0):185-218 PMID: 1094495
  10. Structure of yeast phenylalanine transfer RNA at 2.5 A resolution.
    Proc Natl Acad Sci U S A. 1975 Nov;72(11):4414-8 PMID: 1105583
  11. Hydrogen bonding in yeast phenylalanine transfer RNA.
    Proc Natl Acad Sci U S A. 1975 Dec;72(12):4866-70 PMID: 1108007
  12. Complementary base pairing and the origin of substitution mutations.
    Nature. 1976 Sep 23;263(5575):285-9 PMID: 958482
  13. Base pairing and fidelity in codon-anticodon interaction.
    Nature. 1976 Sep 23;263(5575):289-93 PMID: 958483
  14. Transfer RNA: molecular structure, sequence, and properties.
    Annu Rev Biochem. 1976;45:805-60 PMID: 60910
  15. Structural domains of transfer RNA molecules.
    Science. 1976 Nov 19;194(4267):796-806 PMID: 790568
  16. Crystallographic refinement of yeast phenylalanine transfer RNA at 2-5A resolution.
    J Mol Biol. 1976 Dec 25;108(4):619-49 PMID: 798036
  17. A crystallographic study of metal-binding to yeast phenylalanine transfer RNA.
    J Mol Biol. 1977 Apr 15;111(3):315-28 PMID: 325214
  18. RNA-ligant interactions. (I) Magnesium binding sites in yeast tRNAPhe.
    Nucleic Acids Res. 1977 Aug;4(8):2811-20 PMID: 333395
  19. Initial stages of the thermal unfolding of yeast phenylalanine transfer RNA as studied by chemical modification: the effect of magnesium.
    Eur J Biochem. 1977 Nov 15;81(1):91-101 PMID: 412674
  20. Enzymatic oligoribonucleotide synthesis with T4 RNA ligase.
    Biochemistry. 1978 May 30;17(11):2069-76 PMID: 667012
  21. Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications.
    J Mol Biol. 1978 Aug 25;123(4):631-60 PMID: 357743
  22. Further refinement of the structure of yeast tRNAPhe.
    J Mol Biol. 1978 Sep 25;124(3):523-34 PMID: 361973
  23. Reactions at the termini of tRNA with T4 RNA ligase.
    Nucleic Acids Res. 1978 Oct;5(10):3665-77 PMID: 724498
  24. Direct chemical method for sequencing RNA.
    Proc Natl Acad Sci U S A. 1979 Apr;76(4):1760-4 PMID: 377283
  25. The use of intensifying screens or organic scintillators for visualizing radioactive molecules resolved by gel electrophoresis.
    Methods Enzymol. 1980;65(1):363-71 PMID: 7374459
  26. Different pattern of codon recognition by mammalian mitochondrial tRNAs.
    Proc Natl Acad Sci U S A. 1980 Jun;77(6):3164-6 PMID: 6932013
  27. The sequence of a possible 5S RNA-equivalent in hamster mitochondria.
    Nucleic Acids Res. 1980 Aug 25;8(16):3603-10 PMID: 6159582
  28. Chemical probes for higher-order structure in RNA.
    Proc Natl Acad Sci U S A. 1980 Aug;77(8):4679-82 PMID: 6159633
  29. The nucleotide sequence of a small (3S) seryl-tRNA (anticodon GCU) from beef heart mitochondria.
    Nucleic Acids Res. 1980 Nov 25;8(22):5207-12 PMID: 6906661
  30. A mammalian mitochondrial serine transfer RNA lacking the "dihydrouridine" loop and stem.
    Nucleic Acids Res. 1980 Nov 25;8(22):5213-22 PMID: 6906662
  31. Sequence and organization of the human mitochondrial genome.
    Nature. 1981 Apr 9;290(5806):457-65 PMID: 7219534
  32. Sequence and gene organization of mouse mitochondrial DNA.
    Cell. 1981 Oct;26(2 Pt 2):167-80 PMID: 7332926
  33. Compilation of tRNA sequences.
    Nucleic Acids Res. 1982 Jan 22;10(2):r1-55 PMID: 7063409
  34. Compilation of sequences of tRNA genes.
    Nucleic Acids Res. 1982 Jan 22;10(2):r57-81 PMID: 7063410
  35. Mitochondrial DNA sequences of primates: tempo and mode of evolution.
    J Mol Evol. 1982;18(4):225-39 PMID: 6284948
  36. Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome.
    J Mol Biol. 1982 Apr 25;156(4):683-717 PMID: 7120390
  37. Detailed molecular model for transfer ribonucleic acid.
    Nature. 1969 Nov 22;224(5221):759-63 PMID: 5361649
Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
0261-4189
Published
1983-00-00
Pages
1309-21
Language
English
Region
England
NLM ID
8208664
PMCID
PMC555277
Subset
IM
External Links
PubMed source PMC Full Text View journal details
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