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PDBsum entry 1dwm
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Serine proteinase inhibitor
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PDB id
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1dwm
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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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Determination of a high precision structure of a novel protein, Linum usitatissimum trypsin inhibitor (luti), Using computer-Aided assignment of noesy cross-Peaks.
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Authors
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T.Cierpicki,
J.Otlewski.
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Ref.
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J Mol Biol, 2000,
302,
1179-1192.
[DOI no: ]
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PubMed id
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Abstract
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The solution structure of a novel 69 residue proteinase inhibitor, Linum
usitatissimum trypsin inhibitor (LUTI), was determined using a method based on
computer aided assignment of nuclear Overhauser enhancement spectroscopy (NOESY)
data. The approach applied uses the program NOAH/DYANA for automatic assignment
of NOESY cross-peaks. Calculations were carried out using two unassigned NOESY
peak lists and a set of determined dihedral angle restraints. In addition,
hydrogen bonds involving amide protons were identified during calculations using
geometrical criteria and values of HN temperature coefficients. Stereospecific
assignment of beta-methylene protons was carried out using a standard procedure
based on nuclear Overhauser enhancement intensities and 3J(alpha)(beta) coupling
constants. Further stereospecific assignment of methylene protons and
diastereotopic methyl groups were established upon structure-based method
available in the program GLOMSA and chemical shift calculations. The applied
algorithm allowed us to assign 1968 out of 2164 peaks (91%) derived from NOESY
spectra recorded in H2O and 2H2O. The final experimental data input consisted of
1609 interproton distance restraints, 88 restraints for 44 hydrogen bonds, 63
torsion angle restraints and 32 stereospecifically assigned methylene proton
pairs and methyl groups. The algorithm allowed the calculation of a high
precision protein structure without the laborious manual assignment of NOESY
cross-peaks. For the 20 best conformers selected out of 40 refined ones in the
program CNS, the calculated average pairwise rmsd values for residues 3 to 69
were 0.38 A (backbone atoms) and 1.02 A (all heavy atoms). The three-dimensional
LUTI structure consists of a mixed parallel and antiparallel beta-sheet, a
single alpha-helix and shows the fold of the potato 1 family of proteinase
inhibitors. Compared to known structures of the family, LUTI contains Arg and
Trp residues at positions P6' and P8', respectively, instead of two Arg
residues, involved in the proteinase binding loop stabilization. A consequence
of the ArgTrp substitution at P8' is a slightly more compact conformation of the
loop relative to the protein core.
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Figure 4.
Figure 4. Stereo view showing ribbon representation of LUTI
structure and arrangement of secondary structures. The only
disulfide bridge (Cys4-Cys49) connecting the N terminus with
protein core is shown in green.
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Figure 8.
Figure 8. Stereo view showing superimposition of P[2]-P[1]'
and P[6]'-P[8]' residues of LUTI (averaged 1dwm, shown in red),
CI-2 (2ci2, blue) and eglin c (1acb, cyan).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2000,
302,
1179-1192)
copyright 2000.
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