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PDBsum entry 2bhx
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References listed in PDB file
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Key reference
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Title
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Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage.
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Authors
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A.P.Dubnovitsky,
R.B.Ravelli,
A.N.Popov,
A.C.Papageorgiou.
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Ref.
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Protein Sci, 2005,
14,
1498-1507.
[DOI no: ]
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PubMed id
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Abstract
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The X-ray susceptibility of the lysine-pyridoxal-5'-phosphate Schiff base in
Bacillus alcalophilus phosphoserine aminotransferase has been investigated using
crystallographic data collected at 100 K to 1.3 A resolution, complemented by
on-line spectroscopic studies. X-rays induce deprotonation of the internal
aldimine, changes in the Schiff base conformation, displacement of the cofactor
molecule, and disruption of the Schiff base linkage between
pyridoxal-5'-phosphate and the Lys residue. Analysis of the
"undamaged" structure reveals a significant chemical strain on the
internal aldimine bond that leads to a pronounced geometrical distortion of the
cofactor. However, upon crystal exposure to the X-rays, the strain and
distortion are relaxed and eventually diminished when the total absorbed dose
has exceeded 4.7 x 10(6) Ggamma. Our data provide new insights into the
enzymatic activation of pyridoxal-5'-phosphate and suggest that special care
should be taken while using macromolecular crystallography to study details in
strained active sites.
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Figure 3.
Figure 3. X-ray-induced structural changes in the active
site of BALC PSAT. Sigma A-weighted difference Fourier maps
(wF[A]-wF[n]) between the first data set, A, and the successive
data sets, B-G, respectively, are shown. Superimposed atomic
coordinates from the model A are presented. The green density
represents maps contoured at 6.5  , and the
blue density represents maps contoured at -6.0 . The figure
was produced using BOBSCRIPT (Esnouf 1997) and Raster 3D
(Merritt and Murphy 1994). (A) wF[A]-wF[B] map. (B) wF[A]-wF[C]
map. (C) wF[A]-wF[D] map. (D) wF[A]-wF[E] map. (E) wF[A]-wF[F]
map. (F) wF[A]-wF[G] map.
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Figure 6.
Figure 6. Distortion of pyridoxal-5'-phosphate in the
active site of BALC PSAT. Atomic coordinates of PLP and Lys196
side chain from the model H are presented in black. In gray, the
superimposed planar conformation of the PLP molecule from the
atomic resolution structure of BALC PSAT is shown (PDB accession
code 1W23). The figure was produced using MOLSCRIPT (Kraulis
1991) and Raster 3D (Merritt and Murphy 1994).
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The above figures are
reprinted
by permission from the Protein Society:
Protein Sci
(2005,
14,
1498-1507)
copyright 2005.
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