PDBsum entry 2bc3

Biotin binding protein

PDB id: 2bc3

Contents

Protein chains

145 a.a. *

Ligands

GOL ×2

SO4

Waters ×279

* Residue conservation analysis

PDB id:

2bc3

Name:

Biotin binding protein

Title:

T7-tagged full-length streptavidin

Structure:

Streptavidin. Chain: a, b. Engineered: yes

Source:

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

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.54Å R-factor: 0.179 R-free: 0.243

Authors:

R.E.Stenkamp,I.Le Trong,T.R.Ward,N.Humbert

Key ref:

I.Le Trong et al. (2006). Crystallographic Analysis of a Full-length Streptavidin with Its C-terminal Polypeptide Bound in the Biotin Binding Site. J Mol Biol, 356, 738-745. PubMed id: 16384581 DOI: 10.1016/j.jmb.2005.11.086

Date:

18-Oct-05 Release date: 25-Oct-05

Protein chains

P22629  (SAV_STRAV) -  Streptavidin from Streptomyces avidinii

Seq: 183 a.a.

Struc: 145 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1016/j.jmb.2005.11.086

J Mol Biol 356:738-745 (2006)

PubMed id: 16384581

Crystallographic Analysis of a Full-length Streptavidin with Its C-terminal Polypeptide Bound in the Biotin Binding Site.

I.Le Trong, N.Humbert, T.R.Ward, R.E.Stenkamp.

ABSTRACT

The structure of a full-length streptavidin has been determined at 1.7A resolution and shows that the 20 residue extension at the C terminus forms a well-ordered polypeptide loop on the surface of the tetramer. Residues 150-153 of the extension are bound to the ligand-binding site, possibly competing with exogenous ligands. The binding mode of these residues is compared with that of biotin and peptidic ligands. The observed structure helps to rationalize the observations that full-length mature streptavidin binds biotinylated macromolecules with reduced affinity.

Selected figure(s)

Figure 4.
Figure 4. Stereo view of a subunit of wild-type core-streptavidin (PDB ident 1MK5) (pink coil) superposed on T7-SA (blue coil). Biotin (bound in core-streptavidin) is shown in ball-and-stick representation. The flexible binding loop in the biotin complex is shown in violet. The missing residues in this loop in the open conformation in T7-SA are shown as transparent coil. The major differences between the wild-type and T7-SA structures, in addition to the additional residues at the C terminus, involve the conformation of the flexible binding loop (residues 45-52) and the conformation of residues 24-26 near the a helix.

Figure 8.
Figure 8. Stereo view showing the overlap of the flexible binding loop in the wild-type core-streptavidin-biotin complex (pink bonds) with residues near the C terminus of T7-SA (blue bonds). Residues 154-156 in T7-SA, while not actually bound in the biotin-binding site, take on the same conformation and nearly the same location as the closed loop in the wild-type-biotin complex.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 356, 738-745) copyright 2006.

Figures were selected by the author.