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PDBsum entry 2fvm
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References listed in PDB file
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Key reference
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Title
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The crystal structures of dihydropyrimidinases reaffirm the close relationship between cyclic amidohydrolases and explain their substrate specificity.
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Authors
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B.Lohkamp,
B.Andersen,
J.Piskur,
D.Dobritzsch.
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Ref.
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J Biol Chem, 2006,
281,
13762-13776.
[DOI no: ]
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PubMed id
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Abstract
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In eukaryotes, dihydropyrimidinase catalyzes the second step of the reductive
pyrimidine degradation, the reversible hydrolytic ring opening of
dihydropyrimidines. Here we describe the three-dimensional structures of
dihydropyrimidinase from two eukaryotes, the yeast Saccharomyces kluyveri and
the slime mold Dictyostelium discoideum, determined and refined to 2.4 and 2.05
angstroms, respectively. Both enzymes have a (beta/alpha)8-barrel structural
core embedding the catalytic di-zinc center, which is accompanied by a smaller
beta-sandwich domain. Despite loop-forming insertions in the sequence of the
yeast enzyme, the overall structures and architectures of the active sites of
the dihydropyrimidinases are strikingly similar to each other, as well as to
those of hydantoinases, dihydroorotases, and other members of the amidohydrolase
superfamily of enzymes. However, formation of the physiologically relevant
tetramer shows subtle but nonetheless significant differences. The extension of
one of the sheets of the beta-sandwich domain across a subunit-subunit interface
in yeast dihydropyrimidinase underlines its closer evolutionary relationship to
hydantoinases, whereas the slime mold enzyme shows higher similarity to the
noncatalytic collapsin-response mediator proteins involved in neuron
development. Catalysis is expected to follow a dihydroorotase-like mechanism but
in the opposite direction and with a different substrate. Complexes with
dihydrouracil and N-carbamyl-beta-alanine obtained for the yeast
dihydropyrimidinase reveal the mode of substrate and product binding and allow
conclusions about what determines substrate specificity, stereoselectivity, and
the reaction direction among cyclic amidohydrolases.
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Figure 1.
FIGURE 1. Subunit structures. a, stereo view of the subunit
of ^SkDHPase. The following color coding is used for the
secondary structure elements: green and dark green, barrel
strands and helices, respectively; blue and light blue, strands
of the larger and smaller sheets of the  -sandwich domain,
respectively; yellow, additional -strands; orange and
dark orange, additional  - and 3[10]-helices,
respectively. Spheres in magenta represent the zinc ions of the
metal center. b, stereo view of the subunit of ^DdDHPase. The
same color coding as in a is used. c, stereo view of the
superimposed subunits of ^SkDHPase (light blue), ^DdDHPase
(blue), CRMP1 (gold), and ^B9D-Hyd (magenta). The orientation is
changed for better visualization of the structural differences,
especially at the C terminus, and is related to that from a and
b by a 45° upward rotation around a horizontal axis lying
within the paper plane.
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Figure 3.
FIGURE 3. Structures of the tetramers showing the
intersubunit interfaces. a, tetramer of ^SkDHPase in two
orientations related by a 90° rotation around a 2-fold axis
lying within the paper plane (as indicated), with subunits A, B,
C, and D shown in gold, magenta, blue, and light green. b,
corresponding view of the ^DdDHPase tetramer. Here the subunits
are shown in yellow (A), red (B), light blue (C), and green (D).
The rigid body movement of the dimer pairs in relation to the
corresponding pairs in ^SkDHPase is indicated by an arrow. c,
tetramer of ^B9D-Hyd, with the subunits colored in
correspondence to ^SkDHPase. d, tetramer of CRMP1. The subunit
color code corresponds to that of ^DdDHPase.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
13762-13776)
copyright 2006.
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Secondary reference #1
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Title
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Crystallization and X-Ray diffraction analysis of dihydropyrimidinase from saccharomyces kluyveri
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Authors
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D.Dobritzsch,
B.Andersen,
J.Piskur.
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Ref.
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acta crystallogr ,sect f, 2005,
61,
359.
[DOI no: ]
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PubMed id
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Figure 1.
FIGURE 1. Subunit structures. a, stereo view of the subunit
of ^SkDHPase. The following color coding is used for the
secondary structure elements: green and dark green, barrel
strands and helices, respectively; blue and light blue, strands
of the larger and smaller sheets of the -sandwich domain,
respectively; yellow, additional -strands; orange and
dark orange, additional - and 3[10]-helices,
respectively. Spheres in magenta represent the zinc ions of the
metal center. b, stereo view of the subunit of ^DdDHPase. The
same color coding as in a is used. c, stereo view of the
superimposed subunits of ^SkDHPase (light blue), ^DdDHPase
(blue), CRMP1 (gold), and ^B9D-Hyd (magenta). The orientation is
changed for better visualization of the structural differences,
especially at the C terminus, and is related to that from a and
b by a 45° upward rotation around a horizontal axis lying
within the paper plane.
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Figure 3.
FIGURE 3. Structures of the tetramers showing the
intersubunit interfaces. a, tetramer of ^SkDHPase in two
orientations related by a 90° rotation around a 2-fold axis
lying within the paper plane (as indicated), with subunits A, B,
C, and D shown in gold, magenta, blue, and light green. b,
corresponding view of the ^DdDHPase tetramer. Here the subunits
are shown in yellow (A), red (B), light blue (C), and green (D).
The rigid body movement of the dimer pairs in relation to the
corresponding pairs in ^SkDHPase is indicated by an arrow. c,
tetramer of ^B9D-Hyd, with the subunits colored in
correspondence to ^SkDHPase. d, tetramer of CRMP1. The subunit
color code corresponds to that of ^DdDHPase.
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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