5TUJ | pdb_00005tuj

Ancestral Cationic Amino Acid Solute Binding Protein (AncCDT-1)

• PDB DOI: https://doi.org/10.2210/pdb5TUJ/pdb

• Classification: Solute Binding Protein
• Organism(s): unidentified
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-11-06 Released: 2017-12-06 
• Deposition Author(s): Kaczmarski, J.A., Clifton, B.E., Carr, P.D., Jackson, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 
  0.338 (Depositor), 0.343 (DCC) 
• R-Value Work: 
  0.305 (Depositor), 0.312 (DCC) 
• R-Value Observed: 
  0.307 (Depositor) 

Literature

Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein.

Clifton, B.E., Kaczmarski, J.A., Carr, P.D., Gerth, M.L., Tokuriki, N., Jackson, C.J.

(2018) Nat Chem Biol 14: 542-547

• PubMed: 29686357 
• DOI: https://doi.org/10.1038/s41589-018-0043-2
• Primary Citation Related Structures: 
  5TUJ, 5WJP, 6BQE


• PubMed Abstract: 
  

  The emergence of enzymes through the neofunctionalization of noncatalytic proteins is ultimately responsible for the extraordinary range of biological catalysts observed in nature. Although the evolution of some enzymes from binding proteins can be inferred by homology, we have a limited understanding of the nature of the biochemical and biophysical adaptations along these evolutionary trajectories and the sequence in which they occurred. Here we reconstructed and characterized evolutionary intermediate states linking an ancestral solute-binding protein to the extant enzyme cyclohexadienyl dehydratase. We show how the intrinsic reactivity of a desolvated general acid was harnessed by a series of mutations radiating from the active site, which optimized enzyme-substrate complementarity and transition-state stabilization and minimized sampling of noncatalytic conformations. Our work reveals the molecular evolutionary processes that underlie the emergence of enzymes de novo, which are notably mirrored by recent examples of computational enzyme design and directed evolution.

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Organizational Affiliation: 
• Research School of Chemistry, Australian National University, Canberra, ACT, Australia.
Department of Biochemistry, University of Otago, Dunedin, New Zealand.
School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
Research School of Chemistry, Australian National University, Canberra, ACT, Australia. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.29 kDa 
• Atom Count: 1,738 
• Modeled Residue Count: 229 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ancestral protein CDT-Anc1	A [auth C]	235	unidentified	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free:  0.338 (Depositor), 0.343 (DCC) 
• R-Value Work:  0.305 (Depositor), 0.312 (DCC) 
• R-Value Observed: 0.307 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.641	α = 90
b = 71.641	β = 90
c = 124.001	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Kaczmarski, J.A., Clifton, B.E., Carr, P.D., Jackson, C.J.

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2019-01-16
  Changes: Data collection, Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references