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PDBsum entry 1pn0
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Oxidoreductase
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PDB id
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1pn0
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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High-Resolution structure of phenol hydroxylase and correction of sequence errors.
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Author
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C.Enroth.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2003,
59,
1597-1602.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure model of phenol hydroxylase has been corrected for 11
sequence errors and refined against new data to 1.7 A resolution. The higher
resolution data together with careful exploitation of non-crystallographic
symmetry restraints and the use of many small groups for refinement of
anisotropic displacement parameters resulted in a large decrease in the
crystallographic R factor. The final crystallographic free R factor is 18.0%,
which should be compared with the values of 27.8% for the previously published
model (PDB code 1foh). The rebuilding and re-refinement procedure is described.
A comparison with the previously published model was performed and possible
biochemical implications are discussed. No large differences suggesting gross
errors in the earlier model were found. The actual differences between these two
models give an indication of the level of ambiguity and inaccuracy that may be
found in a well refined protein model at 2.4 A resolution.
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Figure 2.
Figure 2 A figure showing the eight structural domains of a
subunit which were treated as independent domains in the TLS
refinement. FAD, which was treated as another separate TLS
domain, is shown in ball-and-stick representation. This figure
was prepared with MOLSCRIPT (Kraulis, 1991[Kraulis, P. J.
(1991). J. Appl. Cryst. 24, 946-950.]) and Raster3D (Merritt &
Murphy, 1994[Merritt, E. A. & Murphy, M. E. P. (1994). Acta
Cryst. D50, 869-873.]).
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The above figure is
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2003,
59,
1597-1602)
copyright 2003.
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Secondary reference #1
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Title
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The crystal structure of phenol hydroxylase in complex with FAD and phenol provides evidence for a concerted conformational change in the enzyme and its cofactor during catalysis.
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Authors
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C.Enroth,
H.Neujahr,
G.Schneider,
Y.Lindqvist.
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Ref.
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Structure, 1998,
6,
605-617.
[DOI no: ]
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PubMed id
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Figure 6.
Figure 6. Schematic drawing of the FAD-binding site of
phenol hydroxylase in (a) the `in' conformation and (b) the
`out' conformation. The two conformations are stabilised by
hydrogen bonds, but the bonding pattern is significantly
different in the two states. Most notable are the hydrogen bonds
from the isoalloxazine ring to the mainchain nitrogen atoms of
residues Gly55, Gly369, Met370 and Asn371, which are all broken
and in some cases exchanged to hydrogen bonds to water molecules
in the out conformation. Residue His 189 (in (a)), depicted with
an asterisk, is located in the flexible segment of the
polypeptide chain and consequently does not make contacts to FAD
in the out conformation, where the loop is in the open
conformation. In addition, residues 43-52 move slightly between
the two conformations, in concert with the movement of the
isoalloxazine ring. Most notable here is Gln52, which works as a
hinge for this stretch of residues. In the in case Gln52 is
hydrogen bonded to an oxygen atom of the ribityl chain; in the
out case Gln52 has moved its sidechain to lie parallel to the
isoalloxazine ring. A new hydrogen bond is formed from the same
oxygen, but this time to Gln117. Most of the hydrogen bonds to
FAD are conserved for this class of aromatic hydroxylases.
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The above figure is
reproduced from the cited reference
with permission from Cell Press
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