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PDBsum entry 3faq
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Oxidoreductase
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PDB id
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3faq
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References listed in PDB file
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Key reference
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Title
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Structural evidence of substrate specificity in mammalian peroxidases: structure of the thiocyanate complex with lactoperoxidase and its interactions at 2.4 angstrom resolution.
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Authors
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I.A.Sheikh,
A.K.Singh,
N.Singh,
M.Sinha,
S.B.Singh,
A.Bhushan,
P.Kaur,
A.Srinivasan,
S.Sharma,
T.P.Singh.
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Ref.
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J Biol Chem, 2009,
284,
14849-14856.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of the complex of lactoperoxidase (LPO) with its
physiological substrate thiocyanate (SCN-) has been determined at 2.4A
resolution. It revealed that the SCN- ion is bound to LPO in the distal heme
cavity. The observed orientation of SCN- ion shows that the sulfur atom is
closer to the heme iron than the nitrogen atom. The nitrogen atom of SCN- forms
a hydrogen bond with water molecule W6'. This water molecule is stabilized by
two hydrogen bonds with Gln423 NE2 and Phe422 O. In contrast, the placement of
SCN- ion in the structure of myeloperoxidase (MPO) occurs with an opposite
orientation in which the nitrogen atom is closer to the heme iron than the
sulfur atom. The site corresponding to the positions of Gln423, Phe422 O and W6'
in LPO is occupied primarily by the side chain of Phe407 in MPO due to an
entirely different conformation of the loop corresponding to the segment,
Arg418-Phe431 of LPO. This arrangement in MPO does not favour a similar
orientation of SCN- ion. The orientation of the catalytic product OSCN- ion as
reported in the structure of LPO-OSCN- is similar to the orientation of SCN- in
the structure of LPO-SCN-. Similarly, in the structure of LPO-SCN--CN- in which
CN- binds at the position of W1, the position and orientation of SCN- ion are
also identical to that observed in the structure of LPO-SCN-.
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Figure 1.
Difference Fourier |F[o] – F[c]| map indicating the
presence of SCN^– ions in the complex of LPO·SCN^–.
The cutoff on the left of the pearshaped electron density
corresponds to 2σ (blue), and on the right, it is at 9σ (red).
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Figure 2.
Difference Fourier map calculated in the structures of
LPO·SCN^–·CN^– for SCN^– and CN^– ions.
The electron density from the difference Fourier map with 2σ
cutoff on the left and 9σ cutoff on the right. The rod-like
density for the CN^– ion is also observed at the distal heme
side.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2009,
284,
14849-14856)
copyright 2009.
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