streptavindinStreptavidin and its biotin complex at atomic resolution.
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2011 S67(Pt 9):813-21. doi: 10.. Epub
2011 Aug 9.Streptavidin and its biotin complex at atomic resolution.1, , , , , .1Department of Biological Structure, University of Washington, Seattle, USA.AbstractAtomic resolution crystallographic studies of streptavidin and its biotin complex have been carried out at 1.03 and 0.95 ?, respectively. The wild-type protein crystallized with a tetramer in the asymmetric unit, while the crystals of the biotin complex contained two subunits in the asymmetric unit. Comparison of the six subunits shows the various ways in which the protein accommodates ligand binding and different crystal-packing environments. Conformational variation is found in each of the polypeptide loops connecting the eight strands in the β-sandwich subunit, but the largest differences are found in the flexible binding loop (residues 45-52). In three of the unliganded subunits the loop is in an `open' conformation, while in the two subunits binding biotin, as well as in one of the unliganded subunits, this loop `closes' over the biotin-binding site. The `closed' loop contributes to the protein's high affinity for biotin. Analysis of the anisotropic displacement parameters included in the crystallographic models is consistent with the variation found in the loop structures and the view that the dynamic nature of the protein structure contributes to the ability of the protein to bind biotin so tightly.PMID:
[PubMed - indexed for MEDLINE] PMCID: PMC3169315 The SWT and SWTB tetramers. (a) The four crystallographically unique subunits in the SWT tetramer (subunits A, B, C and D) are related by noncrystallographic twofold axes P, Q and R (Hendrickson et al., 1989). Subunit A is shown in red, subunit B in purple, subunit C in green and subunit D in orange. (b) The SWTB tetramer. The A and B subunits (yellow and blue, respectively) are crystallographically unique. Subunits C and D (brown and gray–blue) are related to subunits A and B by a crystallographic dyad coincident with the P axis. This figure was drawn with MolScript (Kraulis, 1991) and RASTER3D (Merritt & Bacon, 1997).Acta Crystallogr D Biol Crystallogr. 2011 September 1;67(Pt 9):813-821.Polypeptide tracing for the SWT and SWTB subunits after superposition on subunit A of SWT. Subunits colored as in Fig. 1. The loops are labeled, as are the N- and C-termini. Biotin bound to the A subunit of SWTB is shown in ball-and-stick representation. This figure was drawn with MolScript (Kraulis, 1991) and RASTER3D (Merritt & Bacon, 1997).Acta Crystallogr D Biol Crystallogr. 2011 September 1;67(Pt 9):813-821.Root-mean-squared (r.m.s.) distances between Cα atoms for 15 pairwise superpositions of six streptavidin subunits. Gray bars denote the eight β-strands in each subunit. The N-terminus, loops and C-terminus are also labeled. This figure was drawn with gnuplot v.4.4 (Williams & Kelley, 2007).Acta Crystallogr D Biol Crystallogr. 2011 September 1;67(Pt 9):813-821.Solvent-accessible surfaces. (a) Solvent-accessible surface for an isolated A subunit of SWT. As in Fig. 3, the gray bars denote the β-strands. (b) Solvent-accessible surface buried by formation of the SWT tetramer. Buried surfaces for residues in each of the P, Q and R interfaces (see Fig. 1
a) are shown in green, red and blue, respectively. (c) Solvent-accessible surface for an isolated A subunit of SWTB. Small changes are associated with biotin binding. (d) Buried solvent-accessible surface upon formation of the SWTB tetramer. This figure was drawn with gnuplot v.4.4 (Williams & Kelley, 2007).Acta Crystallogr D Biol Crystallogr. 2011 September 1;67(Pt 9):813-821.Average B
eq [= 8π2(U
33)/3] for the main-chain and side-chain atoms. (a) SWT subunits. (b) SWTB subunits. This figure was drawn with gnuplot v.4.4 (Williams & Kelley, 2007).Acta Crystallogr D Biol Crystallogr. 2011 September 1;67(Pt 9):813-821.
eq and anisotropy for residues in the six SWT and SWTB subunits. (a) SWT, subunit A. (b) SWT, subunit B. (c) SWT, subunit C. (d) SWT, subunit D. (e) SWTB, subunit A. (f) SWTB, subunit B. B
eq = 8π2(U
33)/3. The anisotropy values are defined and described in the text. This figure was drawn with gnuplot v.4.4 (Williams & Kelley, 2007).Acta Crystallogr D Biol Crystallogr. 2011 September 1;67(Pt 9):813-821.TLS group boundaries identified for the six streptavidin subunits. Different colored blocks denote different TLS groups identified by the TLSMD server (http://skuld.bmsc.washington.edu/~tlsmd/). Results are shown for ten groups. This figure was drawn with gnuplot v.4.4 (Williams & Kelley, 2007).Acta Crystallogr D Biol Crystallogr. 2011 September 1;67(Pt 9):813-821.Residues making hydrogen bonds to the ureido moiety of biotin. Hydrogen bonds are denoted by green dotted lines. This figure was drawn with MolScript (Kraulis, 1991) and RASTER3D (Merritt & Bacon, 1997).Acta Crystallogr D Biol Crystallogr. 2011 September 1;67(Pt 9):813-821.Publication TypesMeSH TermsSubstancesGrant SupportFull Text SourcesOther Literature SourcesMiscellaneous
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External link. Please review our .Structural studies of hydrogen bonds in the high-affinity streptavidin-biotin complex: mutations of amino acids interacting with the ureido oxygen ...
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2003 S59(Pt 9):1567-73. Epub
2003 Aug 19.Structural studies of hydrogen bonds in the high-affinity streptavidin-biotin complex: mutations of amino acids interacting with the ureido oxygen of biotin.1, , , , , .1Department of Biological Structure and Biomolecular Structure Center, University of Washington, Box 357420, Seattle, Washington , USA.AbstractAn elaborate hydrogen-bonding network contributes to the tight binding of biotin to streptavidin. The specific energetic contributions of hydrogen bonds to the biotin ureido oxygen have previously been investigated by mapping the equilibrium and activation thermodynamic signatures of N23A, N23E, S27A, Y43A and Y43F site-directed mutants [Klumb et al. (1998), Biochemistry, 37, ]. The crystal structures of these variants in the unbound and biotin-bound states provide structural insight into the energetic alterations and are described here. High (1.5-2.2 A) to atomic resolution (1.14 A) structures were obtained and structural models were refined to R values ranging from 0.12 to 0.20. The overall folding of streptavidin as described previously has not changed in any of the mutant structures. Major deviations such as side-chain shifts of residues in the binding site are observed only for the N23A and Y43A mutations. In none of the mutants is a systematic shift of biotin observed when one of the hydrogen-bonding partners to the ureido oxygen of biotin is removed. Recent thermodynamic studies report increases of DeltaDeltaG(o) of 5.0-14.6 kJ mol(-1) for these mutants with respect to the wild-type protein. The decreasing stabilities of the complexes of the mutants are discussed in terms of their structures.PMID:
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