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PDBsum entry 2gkv
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Hydrolase/hydrolase inhibitor
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PDB id
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2gkv
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References listed in PDB file
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Key reference
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Title
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Structural insights into the non-Additivity effects in the sequence-To-Reactivity algorithm for serine peptidases and their inhibitors.
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Authors
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T.W.Lee,
M.A.Qasim,
M.Laskowski,
M.N.James.
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Ref.
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J Mol Biol, 2007,
367,
527-546.
[DOI no: ]
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PubMed id
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Abstract
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Sequence-to-reactivity algorithms (SRAs) for proteins have the potential of
being broadly applied in molecular design. Recently, Laskowski et al. have
reported an additivity-based SRA that accurately predicts most of the standard
free energy changes of association for variants of turkey ovomucoid third domain
(OMTKY3) with six serine peptidases, one of which is streptogrisin B (commonly
known as Streptomyces griseus peptidase B, SGPB). Non-additivity effects for
residues 18I and 32I, and for residues 20I and 32I of OMTKY3 occurred when the
associations with SGPB were predicted using the SRA. To elucidate precisely the
mechanics of these non-additivity effects in structural terms, we have
determined the crystal structures of the unbound OMTKY3 (with Gly32I as in the
wild-type amino acid sequence) at a resolution of 1.16 A, the unbound Ala32I
variant of OMTKY3 at a resolution of 1.23 A, and the SGPB:OMTKY3-Ala32I complex
(equilibrium association constant K(a)=7.1x10(9) M(-1) at 21(+/-2) C degrees, pH
8.3) at a resolution of 1.70 A. Extensive comparisons with the crystal structure
of the unbound OMTKY3 confirm our understanding of some previously addressed
non-additivity effects. Unexpectedly, SGPB and OMTKY3-Ala32I form a 1:2 complex
in the crystal. Comparison with the SGPB:OMTKY3 complex shows a conformational
change in the SGPB:OMTKY3-Ala32I complex, resulting from a hinged rigid-body
rotation of the inhibitor caused by the steric hindrance between the methyl
group of Ala32IA of the inhibitor and Pro192BE of the peptidase. This perturbs
the interactions among residues 18I, 20I, 32I and 36I of the inhibitor, probably
resulting in the above non-additivity effects. This conformational change also
introduces residue 10I as an additional hyper-variable contact residue to the
SRA.
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Figure 3.
Figure 3. Electron density map of the unbound OMTKY3-Ala32I.
(a) 2|F[o]|−|F[c]|,α[c] map of Tyr31I and Ala32I contoured at
3.0σ. (b) 2|F[o]|−|F[c]|,α[c] map of Leu18I and Glu19I
contoured at 1.0σ.
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Figure 5.
Figure 5. Interactions among Thr17I, Glu19I and Arg21I of
ovomucoid third domains under different conditions. (a) Unbound
wtOMSVP3.^12 (b) Unbound OMTKY3. (c) SGPB-bound OMTKY3.^22 (d)
Unbound OMTKY3-Ala32I. (e) Molecule A of OMTKY3-Ala32I in the
SGPB:OMTKY3-Ala32I complex. Hydrogen bonds and ionic
interactions are indicated by dotted lines. Water molecules are
indicated by w.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2007,
367,
527-546)
copyright 2007.
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