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PDBsum entry 1v4p
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References listed in PDB file
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Key reference
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Title
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Crystal structure of alanyl-Trna synthetase editing-Domain homolog (ph0574) from a hyperthermophile, Pyrococcus horikoshii ot3 at 1.45 a resolution.
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Authors
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J.Ishijima,
Y.Uchida,
C.Kuroishi,
C.Tuzuki,
N.Takahashi,
N.Okazaki,
K.Yutani,
M.Miyano.
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Ref.
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Proteins, 2006,
62,
1133-1137.
[DOI no: ]
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PubMed id
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Abstract
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No abstract given.
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Figure 1.
Figure 1. Multiple alignment of the editing domain of AlaRS and
ThrRS enzymes. Residues involved in coordination of the zinc ion
(red) and highly conserved residues (yellow) are indicated. The
secondary structure elements in the crystal structure of PH0574
(above) and ecThrRS (below) are shown in the alignment. GenBank
accession numbers given in parentheses are PH0574 (NP_142539),
mbAlaX (ZP_00296079), pfAlaRS (NP_577999), ecAlaRS (NP_417177),
saThrRS (NP_646443, PDB ID: 1NYR), ecThrRS (NP_416234, PDB ID:
1QF6).
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Figure 2.
Figure 2. (A) Ribbon diagram of PH0574, which consists of a
large (green) domain and a small (orange) domain. The Zn^2+ ion
is located between the two domains. (B) Close-up view of the
Zn^2+ ion binding site. A strong peak in the anomalous
difference Fourier map was observed only at the zinc position.
Many water molecules were observed around the Zn^2+ ion,
although none of these are involved in coordination. The
anomalous difference Fourier map contoured at 20  (orange)
and 2F[o] - F[c] map contoured at 2 (blue)
are shown. (C) Zinc ion coordinate diagram. The coordination of
the Zn^2+ ion is mediated by the conserved histidine and
cysteine residues both in PH0574 (green) and in saThrRS (blue,
parentheses, PDB ID: 1NYR). (D) Structure of the putative active
site drawn with a van der Waals surface with charge. The cavity
accommodates an acyl serine.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2006,
62,
1133-1137)
copyright 2006.
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