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PDBsum entry 1ml1
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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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Protein engineering with monomeric triosephosphate isomerase (monotim): the modelling and structure verification of a seven-Residue loop.
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Authors
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N.Thanki,
J.P.Zeelen,
M.Mathieu,
R.Jaenicke,
R.A.Abagyan,
R.K.Wierenga,
W.Schliebs.
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Ref.
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Protein Eng, 1997,
10,
159-167.
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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
percentage match of
92%.
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Abstract
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Protein engineering experiments have been carried out with loop-1 of monomeric
triosephosphate isomerase (monoTIM). Loop-1 of monoTIM is disordered in every
crystal structure of liganded monoTIM, but in the wild-type TIM it is a very
rigid dimer interface loop. This loop connects the first beta-strand with the
first alpha-helix of the TIM-barrel scaffold. The first residue of this loop,
Lys13, is a conserved catalytic residue. The protein design studies with loop-1
were aimed at rigidifying this loop such that the Lys13 side chain points in the
same direction as seen in wild type. The modelling suggested that the loop
should be made one residue shorter. With the modelling package ICM the optimal
sequence of a new seven-residue loop-1 was determined and its structure was
predicted. The new variant could be expressed and purified and has been
characterized. The catalytic activity and stability are very similar to those of
monoTIM. The crystal structure (at 2.6 A resolution) shows that the experimental
loop-1 structure agrees well with the modelled loop-1 structure. The direct
superposition of the seven loop residues of the modelled and experimental
structures results in an r.m.s. difference of 0.5 A for the 28 main chain atoms.
The good agreement between the predicted structure and the crystal structure
shows that the described modelling protocol can be used successfully for the
reliable prediction of loop structures.
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Secondary reference #1
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Title
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Active site properties of monomeric triosephosphate isomerase (monotim) as deduced from mutational and structural studies.
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Authors
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W.Schliebs,
N.Thanki,
R.Eritja,
R.Wierenga.
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Ref.
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Protein Sci, 1996,
5,
229-239.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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Three new crystal structures of point mutation variants of monotim: conformational flexibility of loop-1, Loop-4 and loop-8.
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Authors
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T.V.Borchert,
K.V.Kishan,
J.P.Zeelen,
W.Schliebs,
N.Thanki,
R.Abagyan,
R.Jaenicke,
R.K.Wierenga.
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Ref.
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Structure, 1995,
3,
669-679.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. (a) The reaction catalyzed by TIM. (b) The structures
of two inhibitors of TIM, PGH and 2PG. Figure 1. (a) The
reaction catalyzed by TIM. (b) The structures of two inhibitors
of TIM, PGH and 2PG.
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Figure 4.
Figure 4. Comparison of monoTIM-SS (red), monoTIM (green) and
wtTIM (yellow). (a) The complete Cα traces. One residue of each
front loop of monoTIM is labelled: Trp12 (L1), Phe45 (L2),
Ala70 (L3), His95 (L4), Glu129 (L5), Val169 (L6), Gly212 (L7)
and Gly235 (L8). Also shown, in green, is the sulphate ion,
near loop-6, loop-7 and loop-8, as observed in the monoTIM
structure. (b) Comparison of the Cα traces near L8, L1, L2 and
L3. The side chains of residues Ser237 (L8), Trp12 (L1), Thr44
(L2) and Gln65 (L3) are also shown. Figure 4. Comparison of
monoTIM-SS (red), monoTIM (green) and wtTIM (yellow). (a) The
complete Cα traces. One residue of each front loop of monoTIM
is labelled: Trp12 (L1), Phe45 (L2), Ala70 (L3), His95 (L4),
Glu129 (L5), Val169 (L6), Gly212 (L7) and Gly235 (L8). Also
shown, in green, is the sulphate ion, near loop-6, loop-7 and
loop-8, as observed in the monoTIM structure. (b) Comparison of
the Cα traces near L8, L1, L2 and L3. The side chains of
residues Ser237 (L8), Trp12 (L1), Thr44 (L2) and Gln65 (L3) are
also shown.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #3
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Title
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The crystal structure of an engineered monomeric triosephosphate isomerase, Monotim: the correct modelling of an eight-Residue loop.
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Authors
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T.V.Borchert,
R.Abagyan,
K.V.Kishan,
J.P.Zeelen,
R.K.Wierenga.
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Ref.
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Structure, 1993,
1,
205-213.
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PubMed id
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