2Y3F

Traptavidin, biotin bound form

Summary for 2Y3F

• Entry DOI: 10.2210/pdb2y3f/pdb
• Related: 1DF8 1HQQ 1HXL 1HXZ 1HY2 1I9H 1KFF 1KL3 1KL4 1KL5 1LCV 1LCW 1LCZ 1LUQ 1MEP 1MK5 1MM9 1MOY 1N43 1N4J 1N7Y 1N9M 1N9Y 1NBX 1NC9 1NDJ 1NQM 1PTS 1RST 1RSU 1RXH 1RXJ 1RXK 1SLD 1SLE 1SLF 1SLG 1SRE 1SRF 1SRG 1SRH 1SRI 1SRJ 1STP 1STR 1STS 1SWA 1SWB 1SWC 1SWD 1SWE 1SWF 1SWG 1SWH 1SWJ 1SWK 1SWL 1SWN 1SWO 1SWP 1SWQ 1SWR 1SWS 1SWT 1SWU 1VWA 1VWB 1VWC 1VWD 1VWE 1VWF 1VWG 1VWH 1VWI 1VWJ 1VWK 1VWL 1VWM 1VWN 1VWO 1VWP 1VWQ 1VWR 2BC3 2F01 2IZA 2IZB 2IZC 2IZD 2IZE 2IZF 2IZG 2IZH 2IZI 2IZJ 2IZK 2IZL 2RTA 2RTB 2RTC 2RTD 2RTE 2RTF 2RTG 2RTH 2RTI 2RTJ 2RTK 2RTL 2RTM 2RTN 2RTO 2RTP 2RTQ 2RTR 2WPU 2Y3E
• Descriptor: STREPTAVIDIN, BIOTIN, GLYCEROL, ... (4 entities in total)
• Functional Keywords: biotin-binding protein, protein engineering
• Biological source: STREPTOMYCES AVIDINII
• Cellular location: Secreted: P22629
• Total number of polymer chains: 1
• Total formula weight: 14689.87

Authors

Chivers, C.E.,Koner, A.L.,Lowe, E.D.,Howarth, M. (deposition date: 2010-12-20, release date: 2011-02-16, Last modification date: 2023-12-20)

Primary citation

Chivers, C.E.,Koner, A.L.,Lowe, E.D.,Howarth, M.
How the Biotin-Streptavidin Interaction Was Made Even Stronger: Investigation Via Crystallography and a Chimeric Tetramer.
Biochem.J., 435:55-, 2011

PubMed Abstract: The interaction between SA (streptavidin) and biotin is one of the strongest non-covalent interactions in Nature. SA is a widely used tool and a paradigm for protein-ligand interactions. We previously developed a SA mutant, termed Tr (traptavidin), possessing a 10-fold lower off-rate for biotin, with increased mechanical and thermal stability. In the present study, we determined the crystal structures of apo-Tr and biotin-Tr at 1.5 Å resolution. In apo-SA the loop (L3/4), near biotin's valeryl tail, is typically disordered and open, but closes upon biotin binding. In contrast, L3/4 was shut in both apo-Tr and biotin-Tr. The reduced flexibility of L3/4 and decreased conformational change on biotin binding provide an explanation for Tr's reduced biotin off- and on-rates. L3/4 includes Ser45, which forms a hydrogen bond to biotin consistently in Tr, but erratically in SA. Reduced breakage of the biotin-Ser45 hydrogen bond in Tr is likely to inhibit the initiating event in biotin's dissociation pathway. We generated a Tr with a single biotin-binding site rather than four, which showed a simi-larly low off-rate, demonstrating that Tr's low off-rate was governed by intrasubunit effects. Understanding the structural features of this tenacious interaction may assist the design of even stronger affinity tags and inhibitors.

PubMed: 21241253
DOI: 10.1042/BJ20101593

Experimental method

X-RAY DIFFRACTION (1.493 Å)