Yeast tRNAPhe: A Tour of the Structure
Introduction: This Chime-based tutorial displays the secondary and
tertiary structural features of yeast tRNAPhe. It is designed
to complement the description in Saenger, W. (1984) Principles of Nucleic
Acid Structure Ch. 15 "tRNA-A Treasury of Stereochemical Information".
It is also based on the figures and descriptions in:
Sussman, J.L. et al. (1978) "Crystal Structure of Yeast Phenylalanine Transfer RNA I. Crystallographic Refinement" J. Mol. Biol. 123 607.
Holbrook, S.R. et al. (1978) "II. Structural Features and Functional Implications." J. Mol. Biol. 123 631.
Most of the tRNA Tour uses the "tRNA.pdb" coordinate file. This is the
PDB-deposited "6TNA" file without H2O and without Mg2+.
In addition, the average B-factors for phosphate groups (from Sussman,
et al. ) were added to each of the P ATOM lines for display in Selection
3.
The close up views of teriary interactions in Selection 4 used RasMol-generated
pdb files that include one residue on either side of the highlighted nucleotides.
| Residue
Number |
PDB
Abbrev. |
Full Name of Nucleoside | Standard
Abbrev. |
|---|---|---|---|
| 10 | 2MG | N2-Methylguanosine | M2G |
| 16 & 17 | H2U | Dihydrouridine | D or hU |
| 26 | M2G | N2, N2-Dimethylguanosine | M22G |
| 32 | OMC | 2'-0-Methylcytidine | M2'C |
| 34 | OMG | 2'-0-Methylguanosine | M2'G |
| 37 | YG | Wybutosine* | Y-base |
| 39 & 55 | PSU | Pseudouridine | Y "Psi" |
| 40 & 49 | 5MC | 5-Methylcytidine | M5C |
| 46 | 7MG | 7-Methyguanosine | M7G |
| 54 | 5MU | 5-Methyluridine | T |
| 58 | 1MA | 1-Methyadenosine | M1A |
These three-letter abbreviations appear on the images when the indicated
residues are labeled. All other residues are identified as the standard
A, C, G, or U nucleotides.
*From the header (remark 5) of 6tna.pdb: "The modified base
(Y-base) in this tRNA is commonly called 'wybutosine'. The systematic name
for the base part of this nucleotide is 1H-Imidazo(1,2-alpha)purine-7-5
butanoic acid,4,9-dihydro-alpha-((methoxycarbonyl)amino)-5 4,6-dimethyl-9-oxo-methyl
Ester. In reality the preceeding is a highly modified guanosine. It is
linked to the ribose via the standard N9-C1' bond."!
A compilation of many other RNA modifications can be found at The
RNA Modification Database.
Please note: The images displayed in this tutorial require the
Chemscape Chime
plug-in. In addition to simply displaying the molecular structures on a
WWW page, the Chime plug-in allows the viewer to manipulate the image with
pull-down menu choices, mouse and keyboard actions, and button-clicks.
A demonstration of these additional features can be found at the Chime
Features page.
Go to the tRNA Structure Tutorial
[This tutorial is also available as a "RasMol animation", i.e. a set of linked scripts that can be run on a computer using the RasMol v2.6 program. A description of the animation and downloading instructions are on the RasMol Animation page.]
Back to Molecular Models for Biochemistry at CMU.
Dr. William McClure
wm0p@andrew.cmu.edu.
Department of Biological Sciences
Carnegie Mellon University
Pittsburgh, PA 15213