Last common ancestor of Gram-negative bacteria (GNCA4) beta-lactamase class A

Experimental Data Snapshot

  • Resolution: 2.12 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


De novo active sites for resurrected Precambrian enzymes.

Risso, V.A.Martinez-Rodriguez, S.Candel, A.M.Kruger, D.M.Pantoja-Uceda, D.Ortega-Munoz, M.Santoyo-Gonzalez, F.Gaucher, E.A.Kamerlin, S.C.L.Bruix, M.Gavira, J.A.Sanchez-Ruiz, J.M.

(2017) Nat Commun 8: 16113-16113

  • DOI: https://doi.org/10.1038/ncomms16113
  • Primary Citation of Related Structures:  
    4UHU, 5FQI, 5FQJ, 5FQK, 5FQM, 5FQQ

  • PubMed Abstract: 

    Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.

  • Organizational Affiliation

    Departamento de Quimica Fisica, Facultad de Ciencias University of Granada, 18071 Granada, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GNCA4 LACTAMASE269synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PG0

Download Ideal Coordinates CCD File 
C5 H12 O3
Query on PEG

Download Ideal Coordinates CCD File 
C4 H10 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.12 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.338α = 90
b = 49.338β = 90
c = 199.114γ = 120
Software Package:
Software NamePurpose
AutoPROCdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Database references
  • Version 1.2: 2019-03-06
    Changes: Data collection, Experimental preparation