3RDM

Crystal structure of R7-2 streptavidin complexed with biotin/PEG

Summary for 3RDM

• Entry DOI: 10.2210/pdb3rdm/pdb
• Related: 3RDO 3RDQ 3RDS 3RDU 3RDX 3RE5 3RE6
• Descriptor: Streptavidin, PENTAETHYLENE GLYCOL, BIOTIN, ... (4 entities in total)
• Functional Keywords: streptavidin variants, improved desthiobiotin binding, opened loop destabilization, biotin binding protein
• Biological source: Streptomyces avidinii
• Cellular location: Secreted: P22629
• Total number of polymer chains: 1
• Total formula weight: 16448.97

Authors

Malashkevich, V.N.,Magalhaes, M.,Czecster, C.M.,Guan, R.,Levy, M.,Almo, S.C. (deposition date: 2011-04-01, release date: 2011-07-06, Last modification date: 2023-09-13)

Primary citation

Magalhaes, M.L.,Czekster, C.M.,Guan, R.,Malashkevich, V.N.,Almo, S.C.,Levy, M.
Evolved streptavidin mutants reveal key role of loop residue in high-affinity binding.
Protein Sci., 20:1145-1154, 2011

PubMed Abstract: We have performed a detailed analysis of streptavidin variants with altered specificity towards desthiobiotin. In addition to changes in key residues which widen the ligand binding pocket and accommodate the more structurally flexible desthiobiotin, the data revealed the role of a key, non-active site mutation at the base of the flexible loop (S52G) which slows dissociation of this ligand by approximately sevenfold. Our data suggest that this mutation results in the loss of a stabilizing contact which keeps this loop open and accessible in the absence of ligand. When this mutation was introduced into the wild-type protein, destabilization of the opened loop conferred a ∼10-fold decrease in both the on-rate and off-rate for the ligand biotin-4-fluoroscein. A similar effect was observed when this mutation was added to a monomeric form of this protein. Our results provide key insight into the role of the streptavidin flexible loop in ligand binding and maintaining high affinity interactions.

PubMed: 21520321
DOI: 10.1002/pro.642

Experimental method

X-RAY DIFFRACTION (1.6 Å)