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PDBsum entry 1ub3
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* Residue conservation analysis
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PDB id:
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Lyase
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Title:
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Crystal structure of tetrameric structure of aldolase from thermus thermophilus hb8
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Structure:
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Aldolase protein. Chain: a, b, c, d. Engineered: yes
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Source:
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Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Biol. unit:
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Tetramer (from
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Resolution:
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1.40Å
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R-factor:
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0.202
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R-free:
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0.211
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Authors:
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N.K.Lokanath,M.Miyano,S.Yokoyama,S.Kuramitsu,N.Kunishima,Riken Structural Genomics/proteomics Initiative (Rsgi)
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Key ref:
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N.K.Lokanath
et al.
(2004).
Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability.
Acta Crystallogr D Biol Crystallogr,
60,
1816-1823.
PubMed id:
DOI:
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Date:
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28-Mar-03
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Release date:
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08-Apr-03
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PROCHECK
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Headers
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References
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Q5SJ28
(DEOC_THET8) -
Deoxyribose-phosphate aldolase from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
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Seq:
Struc:
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220 a.a.
211 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.4.1.2.4
- deoxyribose-phosphate aldolase.
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Pathway:
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Deoxyribose-phosphate aldolase
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Reaction:
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2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
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2-deoxy-D-ribose 5-phosphate
Bound ligand (Het Group name = )
corresponds exactly
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=
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D-glyceraldehyde 3-phosphate
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+
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acetaldehyde
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Acta Crystallogr D Biol Crystallogr
60:1816-1823
(2004)
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PubMed id:
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Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability.
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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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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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Selected figure(s)
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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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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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P.K.Dhar,
C.S.Thwin,
K.Tun,
Y.Tsumoto,
S.Maurer-Stroh,
F.Eisenhaber,
and
U.Surana
(2009).
Synthesizing non-natural parts from natural genomic template.
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J Biol Eng,
3,
2.
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A.Pauluhn,
H.Ahmed,
E.Lorentzen,
S.Buchinger,
D.Schomburg,
B.Siebers,
and
E.Pohl
(2008).
Crystal structure and stereochemical studies of KD(P)G aldolase from Thermoproteus tenax.
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Proteins,
72,
35-43.
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PDB codes:
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R.Morita,
H.Ishikawa,
N.Nakagawa,
S.Kuramitsu,
and
R.Masui
(2008).
Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8.
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Proteins,
73,
259-264.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
