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PDBsum entry 3itx
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Isomerase, metal-binding protein
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PDB id
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3itx
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References listed in PDB file
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Key reference
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Title
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Catalytic reaction mechanism of pseudomonas stutzeri l-Rhamnose isomerase deduced from X-Ray structures.
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Authors
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H.Yoshida,
M.Yamaji,
T.Ishii,
K.Izumori,
S.Kamitori.
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Ref.
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Febs J, 2010,
277,
1045-1057.
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PubMed id
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Abstract
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L-Rhamnose isomerase (L-RhI) catalyzes the reversible isomerization of
L-rhamnose to L-rhamnulose. Pseudomonas stutzeril-RhI, with a broad substrate
specificity, can catalyze not only the isomerization of L-rhamnose, but also
that between D-allose and D-psicose. For the aldose-ketose isomerization by
L-RhI, a metal-mediated hydride-shift mechanism has been proposed, but the
catalytic mechanism is still not entirely understood. To elucidate the entire
reaction mechanism, the X-ray structures of P. stutzeril-RhI in an Mn(2+)-bound
form, and of two inactive mutant forms of P. stutzeril-RhI (S329K and D327N) in
a complex with substrate/product, were determined. The structure of the
Mn(2+)-bound enzyme indicated that the catalytic site interconverts between two
forms with the displacement of the metal ion to recognize both pyranose and
furanose ring substrates. Solving the structures of S329K-substrates allowed us
to examine the metal-mediated hydride-shift mechanism of L-RhI in detail. The
structural analysis of D327N-substrates and additional modeling revealed Asp327
to be responsible for the ring opening of furanose, and a water molecule
coordinating with the metal ion to be involved in the ring opening of pyranose.
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Secondary reference #1
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Title
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The structures of l-Rhamnose isomerase from pseudomonas stutzeri in complexes with l-Rhamnose and d-Allose provide insights into broad substrate specificity.
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Authors
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H.Yoshida,
M.Yamada,
Y.Ohyama,
G.Takada,
K.Izumori,
S.Kamitori.
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Ref.
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J Mol Biol, 2007,
365,
1505-1516.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. (a) Chemical structures of l-rhamnose, l-mannose,
l-lyxose, d-ribose, d-allose, d-xylose, d-glucose, and
d-sorbitol are shown in Fischer projection formulas. The enzyme
activities of P. stutzeri L-RhI for them, K[cat]/K[m] (μM^−1
min^−1),^7 are given in parentheses. (b) Schematic diagram of
the proposed metal-mediated hydride shift reaction of L-RhI.
Figure 1. (a) Chemical structures of l-rhamnose, l-mannose,
l-lyxose, d-ribose, d-allose, d-xylose, d-glucose, and
d-sorbitol are shown in Fischer projection formulas. The enzyme
activities of P. stutzeri L-RhI for them, K[cat]/K[m] (μM^−1
min^−1),[3]^7 are given in parentheses. (b) Schematic diagram
of the proposed metal-mediated hydride shift reaction of L-RhI.
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Figure 6.
Figure 6. Stereo view of (a) the metal-binding site of P.
stutzeri L-RhI, and the substrate-binding sites for (b)
l-rhamnose and (c) d-allose illustrated by the program PyMol.
The metal ions are shown as blue spheres and the water molecules
as red spheres. The bound l-rhamnose and d-allose are shown in
blue and orange, respectively. The selected interactions among
amino acid residues, metal ions, and water molecules are
indicated by dotted lines. *Phe66 from a neighbouring molecule
is shown as thin stick bonds. Carbon atoms of substrates are
numbered from 1 to 6 [http://www.pymol.org]. Figure 6. Stereo
view of (a) the metal-binding site of P. stutzeri L-RhI, and the
substrate-binding sites for (b) l-rhamnose and (c) d-allose
illustrated by the program PyMol. The metal ions are shown as
blue spheres and the water molecules as red spheres. The bound
l-rhamnose and d-allose are shown in blue and orange,
respectively. The selected interactions among amino acid
residues, metal ions, and water molecules are indicated by
dotted lines. *Phe66 from a neighbouring molecule is shown as
thin stick bonds. Carbon atoms of substrates are numbered from 1
to 6 [http://www.pymol.org].
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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