4A29

Structure of the engineered retro-aldolase RA95.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.120 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Evolution of a designed retro-aldolase leads to complete active site remodeling.

Giger, L.Caner, S.Obexer, R.Kast, P.Baker, D.Ban, N.Hilvert, D.

(2013) Nat Chem Biol 9: 494-498

  • DOI: 10.1038/nchembio.1276
  • Primary Citation of Related Structures:  
    4A29, 4A2R, 4A2S

  • PubMed Abstract: 
  • Evolutionary advances are often fueled by unanticipated innovation. Directed evolution of a computationally designed enzyme suggests that pronounced molecular changes can also drive the optimization of primitive protein active sites. The specific activity of an artificial retro-aldolase was boosted >4,400-fold by random mutagenesis and screening, affording catalytic efficiencies approaching those of natural enzymes ...

    Evolutionary advances are often fueled by unanticipated innovation. Directed evolution of a computationally designed enzyme suggests that pronounced molecular changes can also drive the optimization of primitive protein active sites. The specific activity of an artificial retro-aldolase was boosted >4,400-fold by random mutagenesis and screening, affording catalytic efficiencies approaching those of natural enzymes. However, structural and mechanistic studies reveal that the engineered catalytic apparatus, consisting of a reactive lysine and an ordered water molecule, was unexpectedly abandoned in favor of a new lysine residue in a substrate-binding pocket created during the optimization process. Structures of the initial in silico design, a mechanistically promiscuous intermediate and one of the most evolved variants highlight the importance of loop mobility and supporting functional groups in the emergence of the new catalytic center. Such internal competition between alternative reactive sites may have characterized the early evolution of many natural enzymes.


    Organizational Affiliation

    Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENGINEERED RETRO-ALDOL ENZYME RA95.0A258synthetic constructMutation(s): 0 
EC: 4.1.1.48
UniProt
Find proteins for Q06121 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q06121 
Go to UniProtKB:  Q06121
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06121
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3NK
Query on 3NK

Download Ideal Coordinates CCD File 
B [auth A]1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE
C15 H14 O3
HGXDFGVHMYOSDC-UHFFFAOYAY
 Ligand Interaction
MLT
Query on MLT

Download Ideal Coordinates CCD File 
C [auth A]D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.120 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.94α = 90
b = 62.59β = 90
c = 79.81γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2013-06-12
    Changes: Database references
  • Version 1.2: 2013-06-19
    Changes: Database references
  • Version 1.3: 2013-07-31
    Changes: Database references
  • Version 1.4: 2019-05-15
    Changes: Data collection, Database references, Derived calculations, Experimental preparation, Other