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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

How Outer Coordination Sphere Modifications Can Impact Metal Structures in Proteins: A Crystallographic Evaluation.

Ruckthong, L.Stuckey, J.A.Pecoraro, V.L.

(2019) Chemistry 25: 6773-6787

  • DOI: 10.1002/chem.201806040
  • Primary Citation of Related Structures:  

  • 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 ...

    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 II , Pb II , and As III result in trigonal planar or trigonal pyramidal geometries; however, spectroscopic studies have shown that Cd II forms three-, four- or five-coordinate Cd II S 3 (OH 2 ) x (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 II S 3 (OH 2 ). Replacement of Cys by Pen restricts thiol rotation, causing a shift in the metal-binding plane, which displaces water, forming Cd II S 3 . Residue d-Leu, above the Cys site, reorients the side chain towards the Cys layer, diminishing the space for water accommodation yielding Cd II S 3 , whereas d-Leu below opens more space, allowing for equal Cd II S 3 (OH 2 ) and Cd II S 3 (OH 2 ) 2 . These studies provide insights into how to control desired metal geometries in metalloproteins by using coded and non-coded amino acids.


    Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Department of Chemistry, Faculty of Science, King Mongkut's University of Technology, Thonburi (KMUTT), Bang Mod, Thung Khru, Bangkok, 10140, Thailand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apo-(GRAND CoilSerL16CL19(DLE))3
A
36N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DLE
Query on DLE
A
D-PEPTIDE LINKINGC6 H13 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.201 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 37.898α = 90.00
b = 37.898β = 90.00
c = 140.667γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesR01ES012236

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-05-08
    Type: Data collection, Database references
  • Version 1.2: 2019-05-22
    Type: Data collection, Database references