4ID4

Crystal structure of chimeric beta-lactamase cTEM-17m


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.115 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Maintenance of Native-like Protein Dynamics May Not Be Required for Engineering Functional Proteins.

Gobeil, S.M.Clouthier, C.M.Park, J.Gagne, D.Berghuis, A.M.Doucet, N.Pelletier, J.N.

(2014) Chem.Biol. 21: 1330-1340

  • DOI: 10.1016/j.chembiol.2014.07.016

  • PubMed Abstract: 
  • Proteins are dynamic systems, and understanding dynamics is critical for fully understanding protein function. Therefore, the question of whether laboratory engineering has an impact on protein dynamics is of general interest. Here, we demonstrate th ...

    Proteins are dynamic systems, and understanding dynamics is critical for fully understanding protein function. Therefore, the question of whether laboratory engineering has an impact on protein dynamics is of general interest. Here, we demonstrate that two homologous, naturally evolved enzymes with high degrees of structural and functional conservation also exhibit conserved dynamics. Their similar set of slow timescale dynamics is highly restricted, consistent with evolutionary conservation of a functionally important feature. However, we also show that dynamics of a laboratory-engineered chimeric enzyme obtained by recombination of the two homologs exhibits striking difference on the millisecond timescale, despite function and high-resolution crystal structure (1.05 Å) being conserved. The laboratory-engineered chimera is thus functionally tolerant to modified dynamics on the timescale of catalytic turnover. Tolerance to dynamic variation implies that maintenance of native-like protein dynamics may not be required when engineering functional proteins.


    Organizational Affiliation

    PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; Département de Biochimie, Université de Montréal, Montréal QC H3T 1J4, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase TEM, Beta-lactamase PSE-4
A
263Pseudomonas aeruginosaEscherichia coli
This entity is chimeric
Mutation(s): 0 
Gene Names: pse4 (carB1), bla, blaT-3, blaT-4, blaT-5, blaT-6
EC: 3.5.2.6 3.5.2.6
Find proteins for P16897 (Pseudomonas aeruginosa)
Go to UniProtKB:  P16897
Find proteins for P62593 (Escherichia coli)
Go to UniProtKB:  P62593
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.115 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.730α = 90.00
b = 58.720β = 90.00
c = 109.300γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
MxDCdata collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-10-29
    Type: Database references
  • Version 1.2: 2014-11-19
    Type: Database references
  • Version 1.3: 2017-08-02
    Type: Refinement description, Source and taxonomy