As written in
Jovine, L., Djordjevic, S. & Rhodes, D. (2000). “The crystal
structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by
Mg(2+) in 15-year old crystals” J Mol Biol 301, 401-414.
"Furthermore, the possibility of a Mg2+-catalysed cleavage of the
phosphodiester bond between H2U16 and H2U17 was also inferred from the
electron density map of the orthorhombic form of the tRNAPhe crystals
[Sussman et al 1978].
n.b. this chain break was seen 31 years ago, also, in fresh crystals.
Sussman, J.L., Holbrook, S.R., Warrant, R.W., Church, G.M. & Kim, S.-
H. (1978). Crystal structure of yeast phenylalanine transfer RNA. I.
crystallographic refinement J Mol Biol 123, 607-630.
see Fig 9c: "Residues 16 and 17. Note the discontinuity between
phosphate 17 and ribose 17. This region is one of the weakest electron
density regions."
-----------------------------------------------------------------
Prof. Joel L. Sussman joel.suss...@weizmann.ac.il
Pickman Prof. of Structural Biology +972 (8) 934 4531 - tel
Department of Structural Biology +972 (8) 934 4159 - fax
Weizmann Institute of Science www.weizmann.ac.il/~joel
Rehovot 76100 ISRAEL www.weizmann.ac.il/ISPC
Proteopedia, www.proteopedia.org (because life has more than 2D)
-----------------------------------------------------------------
On 5 Feb 2009, at 21:48, William G. Scott wrote:
Some things improve with age. Here is one of my favorite stories:
http://tinyurl.com/oldtrna
The crystal structure of yeast phenylalanine tRNA at 2.0 Å
resolution: cleavage by Mg2+ in 15-year old crystals
Luca Jovine, Snezana Djordjevica and Daniela Rhodes
We have re-determined the crystal structure of yeast tRNAPhe to 2.0
Å resolution using 15 year old crystals. The accuracy of the new
structure, due both to higher resolution data and formerly
unavailable refinement methods, consolidates the previous structural
information, but also reveals novel details. In particular, the
water structure around the tightly bound Mg2+ is now clearly
resolved, and hence provides more accurate information on the
geometry of the magnesium-binding sites and the role of water
molecules in coordinating the metal ions to the tRNA. We have
assigned a total of ten magnesium ions and identified a partly
conserved geometry for high-affinity Mg2+ binding. In the electron
density map there is also clear density for a spermine molecule
binding in the major groove of the TΨC arm and also contacting a
symmetry-related tRNA molecule. Interestingly, we have also found
that two specific regions of the tRNA in the crystals are partially
cleaved. The sites of hydrolysis are within the D and anticodon
loops in the vicinity of Mg2+.
On Feb 5, 2009, at 11:11 AM, Edward Snell wrote:
</lurk_mode_off>
</dumb_question_on>
Dear All,
I was recently trying to find references on how age may degrade a
crystal, i.e. grow them and use them or preserve them as fresh as
possible. I seem to remember seeing a couple of papers on this but my
memory is fading and I have been unable to locate them. Can anyone
jog
my memory or tell me if I'm imagining things? I've found plenty on
the
protein prep etc. but nothing on the crystal.
Thanks,
Eddie.
Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Email: esn...@hwi.buffalo.edu Telepathy: 42.2 GHz
Heisenberg was probably here! Crystallization, how quaint!
</dumb_question_off>
</lurk_mode_on>
