Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 29018.54 
• Atom Count: 2153 
• Residue Count: 268 
• Unique protein chains: 1

4UHU

W229D mutant of the last common ancestor of Gram-negative bacteria (GNCA) beta-lactamase class A

• DOI: 10.2210/pdb4UHU/pdb

• Classification: HYDROLASE
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2015-03-25 Released: 2016-04-13 
• Deposition Author(s): Gavira, J.A., Risso, V.A., Martinez-Rodriguez, S., Sanchez-Ruiz, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.305 Å
• R-Value Free: 0.179 
• R-Value Work: 0.162 

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: 10.1038/ncomms16113
• Primary Citation of Related Structures:  
  5FQQ, 5FQM, 5FQK, 5FQJ, 5FQI


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
GNCA LACTAMASE W229D	A	268	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FMT	A	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.305 Å
• R-Value Free: 0.179 
• R-Value Work: 0.162 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 70.138	α = 90.00
b = 50.568	β = 90.00
c = 69.719	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-03-25 
• Released Date: 2016-04-13 
• Deposition Author(s): Gavira, J.A., Risso, V.A., Martinez-Rodriguez, S., Sanchez-Ruiz, J.M.

Revision History 

• Version 1.0: 2016-04-13
  Type: Initial release
• Version 1.1: 2017-07-26
  Type: Database references
• Version 1.2: 2017-08-02
  Type: Database references