6EGM

Crystal Structure of a de novo Three-stranded Coiled Coil Peptide Containing D-Leu in a d-site Position of a Tris-thiolate Binding Site

Summary for 6EGM

• Entry DOI: 10.2210/pdb6egm/pdb
• Descriptor: Apo-(GRAND CoilSerL16CL19(DLE))3, ZINC ION (3 entities in total)
• Functional Keywords: three-stranded coiled coil peptide, d-leu, metalloprotein, engineered protein, de novo protein, d-amino acids
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 4180.21

Authors

Ruckthong, L.,Stuckey, J.A.,Pecoraro, V.L. (deposition date: 2018-08-20, release date: 2019-04-03, Last modification date: 2024-10-16)

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 (1.84 Å)