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 
  • R-Value Observed: 0.116 

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
  • Structures With Same Primary Citation

  • 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; Département de Chimie, Université de Montréal, Montréal QC H3T 1J4, Canada; Center for Green Chemistry and Catalysis (CCVC), Montréal QC H3A 0B8, Canada. Electronic address: joelle.pelletier@umontreal.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase TEM, Beta-lactamase PSE-4
A
263Escherichia coliPseudomonas aeruginosaMutation(s): 0 
Gene Names: blablaT-3blaT-4blaT-5blaT-6carB1pse4
EC: 3.5.2.6
Find proteins for P62593 (Escherichia coli)
Go to UniProtKB:  P62593
Find proteins for P16897 (Pseudomonas aeruginosa)
Go to UniProtKB:  P16897
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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

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 
  • R-Value Observed: 0.116 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.73α = 90
b = 58.72β = 90
c = 109.3γ = 90
Software Package:
Software NamePurpose
MxDCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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