4JO6

Streptavidin complex with SBP-Tag

Summary for 4JO6

• Entry DOI: 10.2210/pdb4jo6/pdb
• Related: 1SWE
• Descriptor: Streptavidin, SBP-Tag (3 entities in total)
• Functional Keywords: homotetramer bound to peptides, biotechnological targeting, biotin and peptide binding, unknown function
• Biological source: Streptomyces avidinii; More
• Cellular location: Secreted: P22629
• Total number of polymer chains: 6
• Total formula weight: 74646.95

Authors

Barrette-Ng, I.H.,Wu, S.C.,Tjia, W.M.,Wong, S.L.,Ng, K.K.S. (deposition date: 2013-03-17, release date: 2013-05-01, Last modification date: 2023-11-08)

Primary citation

Barrette-Ng, I.H.,Wu, S.C.,Tjia, W.M.,Wong, S.L.,Ng, K.K.
The structure of the SBP-Tag-streptavidin complex reveals a novel helical scaffold bridging binding pockets on separate subunits
Acta Crystallogr.,Sect.D, 69:879-887, 2013

PubMed Abstract: The 38-residue SBP-Tag binds to streptavidin more tightly (K(d) -/= 2.5-4.9 nM) than most if not all other known peptide sequences. Crystallographic analysis at 1.75 Å resolution shows that the SBP-Tag binds to streptavidin in an unprecedented manner by simultaneously interacting with biotin-binding pockets from two separate subunits. An N-terminal HVV peptide sequence (residues 12-14) and a C-terminal HPQ sequence (residues 31-33) form the bulk of the direct interactions between the SBP-Tag and the two biotin-binding pockets. Surprisingly, most of the peptide spanning these two sites (residues 17-28) adopts a regular α-helical structure that projects three leucine side chains into a groove formed at the interface between two streptavidin protomers. The crystal structure shows that residues 1-10 and 35-38 of the original SBP-Tag identified through in vitro selection and deletion analysis do not appear to contact streptavidin and thus may not be important for binding. A 25-residue peptide comprising residues 11-34 (SBP-Tag2) was synthesized and shown using surface plasmon resonance to bind streptavidin with very similar affinity and kinetics when compared with the SBP-Tag. The SBP-Tag2 was also added to the C-terminus of β-lactamase and was shown to be just as effective as the full-length SBP-Tag in affinity purification. These results validate the molecular structure of the SBP-Tag-streptavidin complex and establish a minimal bivalent streptavidin-binding tag from which further rational design and optimization can proceed.

PubMed: 23633599
DOI: 10.1107/S0907444913002576

Experimental method

X-RAY DIFFRACTION (1.75 Å)