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PDBsum entry 1ub3
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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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Structure of aldolase from thermus thermophilus hb8 showing the contribution of oligomeric state to thermostability.
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Authors
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N.K.Lokanath,
I.Shiromizu,
N.Ohshima,
Y.Nodake,
M.Sugahara,
S.Yokoyama,
S.Kuramitsu,
M.Miyano,
N.Kunishima.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2004,
60,
1816-1823.
[DOI no: ]
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PubMed id
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Abstract
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2-Deoxyribose-5-phosphate aldolase catalyzes a reversible aldol condensation of
two aldehydes via formation of a covalent Schiff-base intermediate at the active
lysine residue. The crystal structure of 2-deoxyribose-5-phosphate aldolase from
Thermus thermophilus HB8 has been determined with and without the substrate at
atomic resolution. This enzyme, which has a unique homotetramer structure, has
been compared with the previously reported crystal structures of two orthologues
from Escherichia coli and Aeropyrum pernix. In contrast to the similar
alpha/beta-barrel fold of the monomers, substantial quaternary structural
differences are observed between these three enzymes. Further comparison of the
subunit-subunit interface areas of these aldolases showed a clear positive
correlation between the interface area and the living temperature of the source
organism. From these results, it is concluded that the oligomeric state of
2-deoxyribose-5-phosphate aldolase is important for the thermostability and not
for the catalytic function.
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Figure 1.
Figure 1
Ribbon representation of T. thermophilus DERA. (a) Protomer structure of TtDERA. Secondary
structures are labelled. The N- and C-termini are coloured blue and red, respectively. (b)
Tetramer structure of TtDERA. Subunits A, B, C and D are coloured blue, yellow, green and
orange, respectively. Molecular local 222 symmetry is depicted by crystallographic
symbols.
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Figure 4.
Figure 4
(a) Topology diagram of T. thermophilus DERA-substrate (DRP) interactions. The residues
and water molecules involved in the catalysis are coloured green. The substrate is shown
in red. Hydrogen bonds are indicated by dotted lines and lengths are given in Å. (b) The
substrate covalently bound to the pocket of the TIM-barrel strand [165][beta] 6. The
substrate and Lys151 residue are depicted in ball-and-stick representation. (c) The
electron density in the vicinity of the DERA active site with the carbinolamine-bound
model. The 2F[o] - F[c] electron density contoured at 2 [166][sigma] is shown in blue.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2004,
60,
1816-1823)
copyright 2004.
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