6EGL

Crystal Structure of a de Novo Three-stranded Coiled Coil Peptide Containing a D-Leu in the Second Coordination Sphere of a Non-metalated Tris-thiolate Binding Site

Summary for 6EGL

• Entry DOI: 10.2210/pdb6egl/pdb
• Descriptor: Apo-(GRAND CoilSerL12(DLE)L16C)3, ZINC ION, POLYETHYLENE GLYCOL (N=34), ... (4 entities in total)
• Functional Keywords: de novo three-stranded coiled coil peptide, tris-thiolate binding site, engineered protein by d-amino acids, d-leu, de novo protein
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 5710.04

Authors

Ruckthong, L.,Stuckey, J.A.,Pecoraro, V.L. (deposition date: 2018-08-20, release date: 2019-04-03, Last modification date: 2023-10-11)

Primary citation

Ruckthong, L.,Stuckey, J.A.,Pecoraro, V.L.
How Outer Coordination Sphere Modifications Can Impact Metal Structures in Proteins: A Crystallographic Evaluation.
Chemistry, 25:6773-6787, 2019

PubMed Abstract: A challenging objective of de novo metalloprotein design is to control of the outer coordination spheres of an active site to fine tune metal properties. The well-defined three stranded coiled coils, TRI and CoilSer peptides, are used to address this question. Substitution of Cys for Leu yields a thiophilic site within the core. Metals such as Hg , Pb , and As result in trigonal planar or trigonal pyramidal geometries; however, spectroscopic studies have shown that Cd forms three-, four- or five-coordinate Cd S (OH ) (in which x=0-2) when the outer coordination spheres are perturbed. Unfortunately, there has been little crystallographic examination of these proteins to explain the observations. Here, the high-resolution X-ray structures of apo- and mercurated proteins are compared to explain the modifications that lead to metal coordination number and geometry variation. It reveals that Ala substitution for Leu opens a cavity above the Cys site allowing for water excess, facilitating Cd S (OH ). Replacement of Cys by Pen restricts thiol rotation, causing a shift in the metal-binding plane, which displaces water, forming Cd S . Residue d-Leu, above the Cys site, reorients the side chain towards the Cys layer, diminishing the space for water accommodation yielding Cd S , whereas d-Leu below opens more space, allowing for equal Cd S (OH ) and Cd S (OH ) . These studies provide insights into how to control desired metal geometries in metalloproteins by using coded and non-coded amino acids.

PubMed: 30861211
DOI: 10.1002/chem.201806040

Experimental method

X-RAY DIFFRACTION (1.4 Å)