PDBsum entry 3csg

De novo protein, sugar binding protein

PDB id: 3csg

Contents

Protein chain

458 a.a. *

Waters ×284

* Residue conservation analysis

PDB id:

3csg

Name:

De novo protein, sugar binding protein

Title:

Crystal structure of monobody ys1(mbp-74)/maltose binding protein fusion complex

Structure:

Maltose-binding protein monobody ys1 fusion. Chain: a. Synonym: mbp. Maltodextrin-binding protein. Mmbp. Engineered: yes. Other_details: male includes residues 5-370, monobody ys1 371-463

Source:

Escherichia coli, synthetic. Gene: male. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.192 R-free: 0.235

Authors:

R.N.Gilbreth,S.Koide

Key ref:

R.N.Gilbreth et al. (2008). A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces. J Mol Biol, 381, 407-418. PubMed id: 18602117 DOI: 10.1016/j.jmb.2008.06.014

Date:

09-Apr-08 Release date: 22-Jul-08

Protein chain

P0AEX9  (MALE_ECOLI) -  Maltose/maltodextrin-binding periplasmic protein from Escherichia coli (strain K12)

Seq: 396 a.a.

Struc: 458 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.jmb.2008.06.014

J Mol Biol 381:407-418 (2008)

PubMed id: 18602117

A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces.

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

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.

Selected figure(s)

Figure 1.
Fig. 1. The FNfn10 scaffold and loop sequences of MBP-binding monobodies. (a) A schematic of the FNIII scaffold. The seven β-strands are labeled A–G and three loops used for interface design (BC, DE and FG) are labeled. (b) The amino acid sequences of the loop regions of YS-only monobody YS1 and monobodies from the YSX library. For the latter group, the number of times each sequence was recovered is indicated in parentheses. The dissociation constant for MBP as measured by yeast display is also given. Unmutated residues originating from the mutagenesis template are colored gray.

Figure 4.
Fig. 4. The paratope structures of the YS1 and YSX1 monobodies. (a) The surface area buried at the interface of individual residues in the BC and FG loops of YS1 and YSX1. (b) The interface buried surface area contributed by each amino type to the YS1 and YSX1 paratopes. (c and d) Structural details of the YS1 and YSX1 interfaces. The left panels show an overall view of the arrangement of major interface contacts and the right panels show close-up views of these interactions. In these illustrations, MBP is shown as a gray surface/sticks and contacting monobody paratope residues are shown as sticks. The carbon atoms of the FG loop residues are colored green, and those of the BC loop residues cyan. Putative hydrogen bonds are indicated by dashed lines.

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2008, 381, 407-418) copyright 2008.

Figures were selected by an automated process.