5FQQ | pdb_00005fqq

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

• PDB DOI: https://doi.org/10.2210/pdb5FQQ/pdb

• Classification: HYDROLASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-14 Released: 2016-12-28 
• Deposition Author(s): Gavira, J.A., Martinez-Rodriguez, S., Risso, V.A., Sanchez-Ruiz, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.221 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 28719578 
• DOI: https://doi.org/10.1038/ncomms16113
• Primary Citation 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.

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Organizational Affiliation: 
• Departamento de Quimica Fisica, Facultad de Ciencias University of Granada, 18071 Granada, Spain.
Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
Departamento de Quimica Fisica Biologica, Instituto de Quimica Fisica Rocasolano, CSIC, c/Serrano 119, 28006-Madrid, Spain.
Departamento de Quimica Organica, Facultad de Ciencias University of Granada, 18071 Granada, Spain.
School of Biology, School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30322, USA.
Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC-University of Granada Avenida de la Palmeras 4, Granada, 18100 Armilla, Spain.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.23 kDa 
• Atom Count: 2,074 
• Modeled Residue Count: 262 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GNCA4 LACTAMASE	A	269	synthetic construct	Mutation(s): 0  EC: 3.5.2.6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG0	B [auth A]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.221 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.338	α = 90
b = 49.338	β = 90
c = 199.114	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-28 
Deposition Author(s): Gavira, J.A., Martinez-Rodriguez, S., Risso, V.A., Sanchez-Ruiz, J.M.

Revision History  

• 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
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description