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PDBsum entry 1evv
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References listed in PDB file
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Key reference
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Title
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The crystal structure of yeast phenylalanine tRNA at 2.0 a resolution: cleavage by mg(2+) in 15-Year old crystals.
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Authors
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L.Jovine,
S.Djordjevic,
D.Rhodes.
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Ref.
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J Mol Biol, 2000,
301,
401-414.
[DOI no: ]
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PubMed id
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Abstract
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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+).
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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).
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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).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2000,
301,
401-414)
copyright 2000.
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Secondary reference #1
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Title
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High-Resolution X-Ray diffraction studies on a pure species of transfer RNA.
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Authors
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J.E.Ladner,
J.T.Finch,
A.Klug,
B.F.Clark.
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Ref.
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J Mol Biol, 1972,
72,
99.
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PubMed id
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Secondary reference #2
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Title
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Structure of yeast phenylalanine tRNA at 3 a resolution.
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Authors
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J.D.Robertus,
J.E.Ladner,
J.T.Finch,
D.Rhodes,
R.S.Brown,
B.F.Clark,
A.Klug.
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Ref.
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Nature, 1974,
250,
546-551.
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PubMed id
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Secondary reference #3
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Title
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Structure of yeast phenylalanine transfer RNA at 2.5 a resolution.
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Authors
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J.E.Ladner,
A.Jack,
J.D.Robertus,
R.S.Brown,
D.Rhodes,
B.F.Clark,
A.Klug.
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Ref.
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Proc Natl Acad Sci U S A, 1975,
72,
4414-4418.
[DOI no: ]
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PubMed id
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Secondary reference #4
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Title
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Further refinement of the structure of yeast trnaphe.
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Authors
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B.Hingerty,
R.S.Brown,
A.Jack.
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Ref.
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J Mol Biol, 1978,
124,
523-534.
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PubMed id
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Secondary reference #5
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Title
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Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, Coordinated waters, And base-Pair propeller twist angles.
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Authors
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E.Westhof,
M.Sundaralingam.
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Ref.
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Biochemistry, 1986,
25,
4868-4878.
[DOI no: ]
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PubMed id
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Secondary reference #6
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Title
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Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals.
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Authors
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E.Westhof,
P.Dumas,
D.Moras.
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Ref.
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Acta Crystallogr A, 1988,
44,
112-123.
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PubMed id
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Headers
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