5U9T

The Tris-thiolate Zn(II)S3Cl Binding Site Engineered by D-Cysteine Ligands in de Novo Three-stranded Coiled Coil Environment

Summary for 5U9T

• Entry DOI: 10.2210/pdb5u9t/pdb
• Related: 5U9U
• Descriptor: Zn(II)Cl(CoilSer L16(DCY))3 2-, ZINC ION, POLYETHYLENE GLYCOL (N=34), ... (7 entities in total)
• Functional Keywords: de novo three-stranded coiled coil, de novo design, d-amino acids in protein design, d-cysteine, tris-thiolate zn(ii)s3cl complex, de novo protein
• Biological source: synthetic construct
• Total number of polymer chains: 3
• Total formula weight: 28962.93

Authors

Ruckthong, L.,Peacock, A.F.A.,Stuckey, J.A.,Pecoraro, V.L. (deposition date: 2016-12-18, release date: 2017-04-26, Last modification date: 2024-10-09)

Primary citation

Ruckthong, L.,Peacock, A.F.A.,Pascoe, C.E.,Hemmingsen, L.,Stuckey, J.A.,Pecoraro, V.L.
d-Cysteine Ligands Control Metal Geometries within De Novo Designed Three-Stranded Coiled Coils.
Chemistry, 23:8232-8243, 2017

PubMed Abstract: Although metal ion binding to naturally occurring l-amino acid proteins is well documented, understanding the impact of the opposite chirality (d-)amino acids on the structure and stereochemistry of metals is in its infancy. We examine the effect of a d-configuration cysteine within a designed l-amino acid three-stranded coiled coil in order to enforce a precise coordination number on a metal center. The d chirality does not alter the native fold, but the side-chain re-orientation modifies the sterics of the metal binding pocket. l-Cys side chains within the coiled-coil structure have previously been shown to rotate substantially from their preferred positions in the apo structure to create a binding site for a tetra-coordinate metal ion. However, here we show by X-ray crystallography that d-Cys side chains are preorganized within a suitable geometry to bind such a ligand. This is confirmed by comparison of the structure of Zn Cl(CSL16 C) to the published structure of Zn (H O)(GRAND-CSL12AL16 C) . Moreover, spectroscopic analysis indicates that the Cd geometry observed by using l-Cys ligands (a mixture of three- and four-coordinate Cd ) is altered to a single four-coordinate species when d-Cys is present. This work opens a new avenue for the control of the metal site environment in man-made proteins, by simply altering the binding ligand with its mirror-imaged d configuration. Thus, the use of non-coded amino acids in the coordination sphere of a metal promises to be a powerful tool for controlling the properties of future metalloproteins.

PubMed: 28384393
DOI: 10.1002/chem.201700660

Experimental method

X-RAY DIFFRACTION (1.92 Å)