3T6F

Biotin complex of Y54F core streptavidin

Summary for 3T6F

• Entry DOI: 10.2210/pdb3t6f/pdb
• Related: 3T6L
• Descriptor: Streptavidin, BIOTIN, BIOTIN-D-SULFOXIDE, ... (6 entities in total)
• Functional Keywords: biotin binding protein
• Biological source: Streptomyces avidinii
• Cellular location: Secreted: P22629
• Total number of polymer chains: 2
• Total formula weight: 28196.48

Authors

Baugh, L.,Le Trong, I.,Cerutti, D.S.,Mehta, N.,Gulich, S.,Stayton, P.S.,Stenkamp, R.E.,Lybrand, T.P. (deposition date: 2011-07-28, release date: 2011-12-21, Last modification date: 2023-09-13)

Primary citation

Baugh, L.,Le Trong, I.,Cerutti, D.S.,Mehta, N.,Gulich, S.,Stayton, P.S.,Stenkamp, R.E.,Lybrand, T.P.
Second-Contact Shell Mutation Diminishes Streptavidin-Biotin Binding Affinity through Transmitted Effects on Equilibrium Dynamics.
Biochemistry, 51:597-607, 2012

PubMed Abstract: We report a point mutation in the second contact shell of the high-affinity streptavidin-biotin complex that appears to reduce binding affinity through transmitted effects on equilibrium dynamics. The Y54F streptavidin mutation causes a 75-fold loss of binding affinity with 73-fold faster dissociation, a large loss of binding enthalpy (ΔΔH = 3.4 kcal/mol at 37 °C), and a small gain in binding entropy (TΔΔS = 0.7 kcal/mol). The removed Y54 hydroxyl is replaced by a water molecule in the bound structure, but there are no observable changes in structure in the first contact shell and no additional changes surrounding the mutation. Molecular dynamics simulations reveal a large increase in the atomic fluctuation amplitudes for W79, a key biotin contact residue, compared to the fluctuation amplitudes in the wild-type. The increased W79 atomic fluctuation amplitudes are caused by loss of water-mediated hydrogen bonds between the Y54 hydroxyl group and peptide backbone atoms in and near W79. We propose that the increased atomic fluctuation amplitudes diminish the integrity of the W79-biotin interaction and represents a loosening of the "tryptophan collar" that is critical to the slow dissociation and high affinity of streptavidin-biotin binding. These results illustrate how changes in protein dynamics distal to the ligand binding pocket can have a profound impact on ligand binding, even when equilibrium structure is unperturbed.

PubMed: 22145986
DOI: 10.1021/bi201221j

Experimental method

X-RAY DIFFRACTION (1.22 Å)