4GD9

Circular Permuted Streptavidin N49/G48

Summary for 4GD9

• Entry DOI: 10.2210/pdb4gd9/pdb
• Related: 1SWF
• Descriptor: Streptavidin, BIOTIN, SULFATE ION, ... (4 entities in total)
• Functional Keywords: biotin-binding protein, biotin, circular permutation
• Biological source: Streptomyces avidinii; More
• Cellular location: Secreted: P22629
• Total number of polymer chains: 4
• Total formula weight: 55852.45

Authors

Le Trong, I.,Chu, V.,Xing, Y.,Lybrand, T.P.,Stayton, P.S.,Stenkamp, R.E. (deposition date: 2012-07-31, release date: 2013-06-05, Last modification date: 2023-09-13)

Primary citation

Le Trong, I.,Chu, V.,Xing, Y.,Lybrand, T.P.,Stayton, P.S.,Stenkamp, R.E.
Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin.
Acta Crystallogr.,Sect.D, 69:968-977, 2013

PubMed Abstract: Circular permutation of streptavidin was carried out in order to investigate the role of a main-chain amide in stabilizing the high-affinity complex of the protein and biotin. Mutant proteins CP49/48 and CP50/49 were constructed to place new N-termini at residues 49 and 50 in a flexible loop involved in stabilizing the biotin complex. Crystal structures of the two mutants show that half of each loop closes over the binding site, as observed in wild-type streptavidin, while the other half adopts the open conformation found in the unliganded state. The structures are consistent with kinetic and thermodynamic data and indicate that the loop plays a role in enthalpic stabilization of the bound state via the Asn49 amide-biotin hydrogen bond. In wild-type streptavidin, the entropic penalties of immobilizing a flexible portion of the protein to enhance binding are kept to a manageable level by using a contiguous loop of medium length (six residues) which is already constrained by its anchorage to strands of the β-barrel protein. A molecular-dynamics simulation for CP50/49 shows that cleavage of the binding loop results in increased structural fluctuations for Ser45 and that these fluctuations destabilize the streptavidin-biotin complex.

PubMed: 23695241
DOI: 10.1107/S0907444913003855

Experimental method

X-RAY DIFFRACTION (1.5 Å)