1RXH

Crystal structure of streptavidin mutant L124R (M1) complexed with biotinyl p-nitroanilide (BNI)

Summary for 1RXH

• Entry DOI: 10.2210/pdb1rxh/pdb
• Related: 1RXJ 1RXK 1i9h 1ij8
• Descriptor: Streptavidin, 5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE (3 entities in total)
• Functional Keywords: avidin, streptavidin, pseudo enzymatic activity, unknown function
• Biological source: Streptomyces avidinii
• Cellular location: Secreted: P22629
• Total number of polymer chains: 2
• Total formula weight: 27379.58

Authors

Eisenberg-Domovich, Y.,Pazy, Y.,Nir, O.,Raboy, B.,Bayer, E.A.,Wilchek, M.,Livnah, O. (deposition date: 2003-12-18, release date: 2004-05-11, Last modification date: 2024-02-14)

Primary citation

Eisenberg-Domovich, Y.,Pazy, Y.,Nir, O.,Raboy, B.,Bayer, E.A.,Wilchek, M.,Livnah, O.
Structural elements responsible for conversion of streptavidin to a pseudoenzyme
Proc.Natl.Acad.Sci.USA, 101:5916-5921, 2004

PubMed Abstract: Avidin enhances the hydrolysis of biotinyl p-nitrophenyl ester (BNP) under mild alkaline conditions, whereas streptavidin prevents hydrolysis of BNP up to pH 12. Recently, we imposed hydrolytic activity on streptavidin by rational mutagenesis, based on the molecular elements responsible for the hydrolysis by avidin. Three mutants were designed, whereby the desired features, the distinctive L124R point mutation (M1), the L3,4 loop replacement (M2), and the combined mutation (M3), were transferred from avidin to streptavidin. The crystal structures of the mutants, in complex with biotinyl p-nitroanilide (BNA), the stable amide analogue of BNP, were determined. The results demonstrate that the point mutation alone has little effect on hydrolysis, and BNA exhibits a conformation similar to that of streptavidin. Substitution of a lengthier L3,4 loop (from avidin to streptavidin), resulted in an open conformation, thus exposing the ligand to solvent. Moreover, the amide bond of BNA was flipped relative to that of the streptavidin and M1 complexes, thus deflecting the nitro group toward Lys-121. Consequently, the leaving group potential of the nitrophenyl group of BNP is increased, and M2 hydrolyzes BNP at pH values >8.5. To better emulate the hydrolytic potential of avidin, M3 was required. The combination of loop replacement and point mutation served to further increase the leaving group potential by interaction of the nitro group with Arg-124 and Lys-121. The information derived from this study may provide insight into the design of enzymes and transfer of desired properties among homologous proteins.

PubMed: 15079055
DOI: 10.1073/pnas.0308541101

Experimental method

X-RAY DIFFRACTION (2.9 Å)