3CSG

Crystal Structure of Monobody YS1(MBP-74)/Maltose Binding Protein Fusion Complex

Summary for 3CSG

• Entry DOI: 10.2210/pdb3csg/pdb
• Related: 2OBG 3CSB
• Descriptor: Maltose-binding protein Monobody YS1 Fusion (2 entities in total)
• Functional Keywords: engineered binding protein, antibody mimic, synthetic protein interface, minimalist protein interface, de novo protein, sugar binding protein
• Biological source: Escherichia coli, synthetic
• Total number of polymer chains: 1
• Total formula weight: 50501.64

Authors

Gilbreth, R.N.,Koide, S. (deposition date: 2008-04-09, release date: 2008-07-22, Last modification date: 2024-02-21)

Primary citation

Gilbreth, R.N.,Esaki, K.,Koide, A.,Sidhu, S.S.,Koide, S.
A Dominant Conformational Role for Amino Acid Diversity in Minimalist Protein-Protein Interfaces
J.Mol.Biol., 381:407-418, 2008

PubMed Abstract: Recent studies have shown that highly simplified interaction surfaces consisting of combinations of just two amino acids, Tyr and Ser, exhibit high affinity and specificity. The high functional levels of such minimalist interfaces might thus indicate small contributions of greater amino acid diversity seen in natural interfaces. Toward addressing this issue, we have produced a pair of binding proteins built on the fibronectin type III scaffold, termed "monobodies." One monobody contains the Tyr/Ser binary-code interface (termed YS) and the other contains an expanded amino acid diversity interface (YSX), but both bind to an identical target, maltose-binding protein. The YSX monobody bound with higher affinity, a slower off rate and a more favorable enthalpic contribution than the YS monobody. High-resolution X-ray crystal structures revealed that both proteins bound to an essentially identical epitope, providing a unique opportunity to directly investigate the role of amino acid diversity in a protein interaction interface. Surprisingly, Tyr still dominates the YSX paratope and the additional amino acid types are primarily used to conformationally optimize contacts made by tyrosines. Scanning mutagenesis showed that while all contacting Tyr side chains are essential in the YS monobody, the YSX interface was more tolerant to mutations. These results suggest that the conformational, not chemical, diversity of additional types of amino acids provided higher functionality and evolutionary robustness, supporting the dominant role of Tyr and the importance of conformational diversity in forming protein interaction interfaces.

PubMed: 18602117
DOI: 10.1016/j.jmb.2008.06.014

Experimental method

X-RAY DIFFRACTION (1.798 Å)