1LQ7 | pdb_00001lq7

De Novo Designed Protein Model of Radical Enzymes

• PDB DOI: https://doi.org/10.2210/pdb1LQ7/pdb
• BMRB: 5356

• Classification: DE NOVO PROTEIN
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-05-09 Released: 2002-06-05 
• Deposition Author(s): Dai, Q.-H., Tommos, C., Fuentes, E.J., Blomberg, M., Dutton, P.L., Wand, A.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 16 
• Selection Criteria: lowest refinement function penalty, best chemical shift agreement 

Literature

Structure of a De Novo Designed Protein Model of Radical Enzymes

Dai, Q.-H., Tommos, C., Fuentes, E.J., Blomberg, M., Dutton, P.L., Wand, A.J.

(2002) J Am Chem Soc 124: 10952-10953

• PubMed: 12224922 
• DOI: https://doi.org/10.1021/ja0264201
• Primary Citation Related Structures: 
  1LQ7


• PubMed Abstract: 
  

  The use of side chains as catalytic cofactors for protein mediated redox chemistry raises significant mechanistic issues as to how these amino acids are activated toward radical chemistry in a controlled manner. De novo protein design has been used to examine the structural basis for the creation and maintenance of a tryptophanyl radical in a three-helix bundle protein maquette. Here we report the detailed structural analysis of the protein by multidimensional NMR methods. An interesting feature of the structure is an apparent pi-cation interaction involving the sole tryptophan and a lysine side chain. Hybrid density functional calculations support the notion that this interaction raises the reduction potential of the W degrees /WH redox pair and helps explain the redox characteristics of the protein. This model protein system therefore provides a powerful model for exploring the structural basis for controlled radical chemistry in protein.

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Organizational Affiliation: 
• The Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.56 kDa 
• Atom Count: 529 
• Modeled Residue Count: 67 
• Deposited Residue Count: 67 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha3W	A	67	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 16 
• Selection Criteria: lowest refinement function penalty, best chemical shift agreement 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-05 
Deposition Author(s): Dai, Q.-H., Tommos, C., Fuentes, E.J., Blomberg, M., Dutton, P.L., Wand, A.J.

Revision History  

• Version 1.0: 2002-06-05
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection