5U9U

De Novo Three-stranded Coiled Coil Peptide Containing a Tris-thiolate Site Engineered by D-Cysteine Ligands

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

d-Cysteine Ligands Control Metal Geometries within De Novo Designed Three-Stranded Coiled Coils.

Ruckthong, L., Peacock, A.F.A., Pascoe, C.E., Hemmingsen, L., Stuckey, J.A., Pecoraro, V.L.

(2017) Chemistry 23: 8232-8243

  • DOI: https://doi.org/10.1002/chem.201700660
  • Primary Citation of Related Structures:  
    5U9T, 5U9U

  • 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 II Cl(CSL16 D C) 3 2- to the published structure of Zn II (H 2 O)(GRAND-CSL12AL16 L C) 3 - . Moreover, spectroscopic analysis indicates that the Cd II geometry observed by using l-Cys ligands (a mixture of three- and four-coordinate Cd II ) 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.

    • Organizational Affiliation: 

    Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apo-(CoilSer L16(DCY))3
A, B, C
31synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.327α = 90
b = 67.517β = 90
c = 69.034γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesES012236

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references, Refinement description
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description