PDBsum entry 1evv

RNA

PDB id: 1evv

Contents

DNA/RNA

Ligands

SPM

Metals

_MG ×10

Waters ×220

PDB id:

1evv

Name:

RNA

Title:

Crystal structure of yeast phenylalanine transfer RNA at 2.0 a resolution

Structure:

Phenylalanine transfer RNA. Chain: a

Source:

Saccharomyces. Organism_taxid: 4930

Resolution:

2.00Å R-factor: 0.227 R-free: 0.263

Authors:

L.Jovine,S.Djordjevic,D.Rhodes

Key ref:

L.Jovine et al. (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. PubMed id: 10926517 DOI: 10.1006/jmbi.2000.3950

Date:

20-Apr-00 Release date: 01-May-00

DNA/RNA chain

G-C-G-G-A-U-U-U-A-2MG-C-U-C-A-G-H2U-H2U-G-G-G-A-G-A-G-C-M2G-C-C-A-G-A-OMC-U-OM 76 bases

DOI no: 10.1006/jmbi.2000.3950

J Mol Biol 301:401-414 (2000)

PubMed id: 10926517

The crystal structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by Mg(2+) in 15-year old crystals.

L.Jovine, S.Djordjevic, D.Rhodes.

ABSTRACT

We have re-determined the crystal structure of yeast tRNA(Phe) to 2. 0 A 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 Mg(2+) 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 Mg(2+ )binding. In the electron density map there is also clear density for a spermine molecule binding in the major groove of the TPsiC 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 Mg(2+).

Selected figure(s)

Figure 2.
Figure 2. Gallery of triple and tertiary base-pairs in the three-dimensional structure of yeast tRNA^Phe. (a) Stick representation of triple base-pairs shown within their combined, sigmaa-weighted |2F[o] - F[c]| electron density map contoured at 1.0 s. Phosphate atoms are shown in magenta, carbon atoms in yellow, nitrogen atoms in blue and oxygen atoms in red. Nucleotide labels are colour coded according to the scheme in Figure 1(a). Mg2+ and water molecules are indicated by green and red spheres, respectively. For clarity, only hydrogen bonds between nucleotides are shown (broken green lines). (b) Stick representation of tertiary base-pairs shown within their combined, sigmaa-weighted |2F[o] - F[c]| electron density map contoured at 1.0 s. Conventions are as in (a).

Figure 3.
Figure 3. The four-strong Mg2+-binding sites in yeast tRNA^Phe. (a) Mg2+-binding site 1, (b) Mg2+-binding site 2, (c) Mg2+-binding site 3, (d) Mg2+-binding site 4. For each site, a stereo representation with combined, sigmaa-weighted |2F[o] - F[c]| electron density map contoured at 1.0 s is shown on the left; on the right, the same binding sites are shown colour-coded according to temperature factors. Conventions are as described in legend to Figure 2. Direct bonds ( slant 2.1 Å) involving Mg2+ ions are shown as continuous black lines, with the exception of the longer range contacts made by Mg2+ 1 (a), which are depicted as broken black lines. The bases of nucleotides G18 and G19 have been omitted for clarity from (c).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 301, 401-414) copyright 2000.

Figures were selected by an automated process.