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PDBsum entry 1tpf
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Isomerase(intramolecular oxidoreductase)
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PDB id
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1tpf
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References listed in PDB file
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Key reference
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Title
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Comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four different crystal forms.
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Authors
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K.V.Kishan,
J.P.Zeelen,
M.E.Noble,
T.V.Borchert,
R.K.Wierenga.
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Ref.
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Protein Sci, 1994,
3,
779-787.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
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Abstract
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Triosephosphate isomerase (TIM) is a dimeric enzyme consisting of 2 identical
subunits. Trypanosomal TIM can be crystallized in 4 different spacegroups:
P2(1)2(1)2(1), C2(big cell), C2(small cell), and P1. The P1 crystal form only
grows in the presence of 1.4 M DMSO; there are 2 DMSO binding sites per subunit.
The structures have been refined at a resolution of 1.83 A, 2.10 A, 2.13 A, and
1.80 A, respectively. In the 4 different spacegroups the TIM subunit can be
observed in the context of 7 different crystallographic environments. In the C2
cells, the dimer 2-fold axis coincides with a crystallographic 2-fold axis. The
similarities and differences of the 7 subunits are discussed. In 6 subunits the
flexible loop (loop 6) is open, whereas in the P2(1)2(1)2(1) cell, the flexible
loop of subunit 2 is in an almost closed conformation. The crystal contacts in
the 4 different crystal forms are predominantly generated by polar residues in
loops. A statistical analysis of the residues involved in crystal contacts shows
that, in particular, serines are frequently involved in these interactions; 19%
of the exposed serines are involved in crystal contacts.
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Figure 2.
Fig. 2. Superposition of the7different
loop 6structures.Thedeviating loop 6
structureisthe closed structure as ob-
servedinsubunit of theP212121form.
Glu 167is one of theactivesiteresdues.
Residues172-175 move asarigid ody
(Wierengaet al., 1991a).
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Figure 3.
Fig. 3. Residuesinvolvedin crystal con-
tacts in the 4 different crysta! forms. The
cut-off value usedwas 3.5 A, therefore
only tight crystal contact interactions have
been considered. The labeled secondary
structure elements identify the@-strands
and a-helics of the 8 (&)-units. At the
bottom f he figure: Ntot(residues)
counts the total number ofresiduesin the
4 different secondary structure elements.
Ntot(contacts)countsthe accumulated
number of crystal contact residues per
type of secondary structure. The loops be-
forethe @-strands are located at he back
side of thesubunit,far frm the active
site; theloopsafterthe@-strandsare at
thefront side of thesubunit, near the ac-
tivesite (loop 1-loop 8) and near the di-
mer interface (loop 1-loop 4).
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(1994,
3,
779-787)
copyright 1994.
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