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PDBsum entry 1xvm
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References listed in PDB file
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Key reference
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Title
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Extraction of functional motion in trypsin crystal structures.
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Authors
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A.Schmidt,
V.S.Lamzin.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2005,
61,
1132-1139.
[DOI no: ]
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PubMed id
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Abstract
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The analysis of anisotropic atomic displacement parameters for the direct
extraction of functionally relevant motion from X-ray crystal structures of
Fusarium oxysporum trypsin is presented. Several atomic resolution structures
complexed with inhibitors or substrates and determined at different pH values
and temperatures were investigated. The analysis revealed a breathing-like
molecular motion conserved across trypsin structures from two organisms and
three different crystal forms. Directional motion was observed suggesting a
change of the width of the substrate-binding cleft and a change in the length of
the specificity pocket. The differences in direction of motion across the
structures are dependent on the mode of substrate or inhibitor binding and the
chemical environment around the active-site residues. Together with the
occurrence of multiple-residue conformers, they reflect spatial rearrangement
throughout the deacylation pathway.
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Figure 1.
Figure 1
Active site in F. oxysporum trypsin. The top row shows the change in the interaction
between the substrate and the catalytic serine and histidine, as well as Asp189 in the
specificity pocket in the ROOM, PH4 and PH5 structures. The distances of interest around
the substrate carbonyl group and in the specificity pocket are shown by dotted lines with
their lengths given in angstroms. W1 and W2 are two water molecules located in the active
site: W1 acts as the nucleophile and W2 as an activator by forming a strong hydrogen bond
to the substrate carbonyl O atom. In the bottom row, the same arrangement of residues is
shown. The protein atoms and coordinate axes are represented and coloured following the
same scheme as in Fig. 3[107] [link]-[108][turqarr.gif] to indicate their directional
motion. The orientation is the same as in Fig. 3[109] [link]-[110][turqarr.gif] . The
figure was created with MOLSCRIPT/RASTER3D (Kraulis, 1991[111] [Kraulis, P. J. (1991). J.
Appl. Cryst. 24, 946-950.]-[112][bluearr.gif] ; Merritt & Murphy, 1994[113] [Merritt, E.
A. & Murphy, M. E. (1994). Acta Cryst. D50, 869-873.]-[114][bluearr.gif] ).
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Figure 2.
Figure 2
Trypsin structures with the degree of anisotropy (average per residue) mapped onto the C^
[137][alpha] trace. The figure was produced with GRASP (Nicholls et al., 1991[138]
[Nicholls, A., Sharp, K. A. & Honig, B. (1991). Proteins, 11, 281-296.]-[139][bluearr.gif]
). The deacylation pathway is depicted on the right-hand side of the figure.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2005,
61,
1132-1139)
copyright 2005.
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