3CSG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.798 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Dominant Conformational Role for Amino Acid Diversity in Minimalist Protein-Protein Interfaces

Gilbreth, R.N.Esaki, K.Koide, A.Sidhu, S.S.Koide, S.

(2008) J.Mol.Biol. 381: 407-418

  • DOI: 10.1016/j.jmb.2008.06.014
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Related Citations: 
    • High affinity single-domain binding proteins with a binary code interface
      Koide, A.,Gilbreth, R.N.,Esaki, K.,Tereshko, V.,Koide, S.
      (2007) Proc.Natl.Acad.Sci.USA 104: 6632


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding protein Monobody YS1 Fusion
A
461Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: malE
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.798 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 68.578α = 90.00
b = 68.578β = 90.00
c = 108.002γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description