PDBsum entry 4gda

Biotin-binding protein

PDB id: 4gda

Contents

Protein chains

124 a.a.

Ligands

BTN ×2

GOL ×3

SO4 ×3

EOH

Waters ×372

PDB id:

4gda

Name:

Biotin-binding protein

Title:

Circular permuted streptavidin a50/n49

Structure:

Streptavidin. Chain: a, b. Engineered: yes

Source:

Streptomyces avidinii. Organism_taxid: 1895. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.00Å R-factor: 0.120 R-free: 0.143

Authors:

I.Le Trong,V.Chu,Y.Xing,T.P.Lybrand,P.S.Stayton,R.E.Stenkamp

Key ref:

I.Le Trong et al. (2013). Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin. Acta Crystallogr D Biol Crystallogr, 69, 968-977. PubMed id: 23695241

Date:

31-Jul-12 Release date: 05-Jun-13

Protein chains

P22629  (SAV_STRAV) -  Streptavidin from Streptomyces avidinii

Seq: 183 a.a.

Struc: 124 a.a.*

* PDB and UniProt seqs differ at 22 residue positions (black crosses)

Acta Crystallogr D Biol Crystallogr 69:968-977 (2013)

PubMed id: 23695241

Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin.

I.Le Trong, V.Chu, Y.Xing, T.P.Lybrand, P.S.Stayton, R.E.Stenkamp.

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.