5W75

Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.298 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and Dynamics Comparison of Thermostability in Ancient, Modern, and Consensus Elongation Factor Tus.

Okafor, C.D.Pathak, M.C.Fagan, C.E.Bauer, N.C.Cole, M.F.Gaucher, E.A.Ortlund, E.A.

(2018) Structure 26: 118-129.e3

  • DOI: 10.1016/j.str.2017.11.018
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Rationally engineering thermostability in proteins would create enzymes and receptors that function under harsh industrial applications. Several sequence-based approaches can generate thermostable variants of mesophilic proteins. To gain insight into ...

    Rationally engineering thermostability in proteins would create enzymes and receptors that function under harsh industrial applications. Several sequence-based approaches can generate thermostable variants of mesophilic proteins. To gain insight into the mechanisms by which proteins become more stable, we use structural and dynamic analyses to compare two popular approaches, ancestral sequence reconstruction (ASR) and the consensus method, used to generate thermostable variants of Elongation Factor Thermo-unstable (EF-Tu). We present crystal structures of ancestral and consensus EF-Tus, accompanied by molecular dynamics simulations aimed at probing the strategies employed to enhance thermostability. All proteins adopt crystal structures similar to extant EF-Tus, revealing no difference in average structure between the methods. Molecular dynamics reveals that ASR-generated sequences retain dynamic properties similar to extant, thermostable EF-Tu from Thermus aquaticus, while consensus EF-Tu dynamics differ from evolution-based sequences. This work highlights the advantage of ASR for engineering thermostability while preserving natural motions in multidomain proteins.


    Organizational Affiliation

    School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA. Electronic address: eortlun@emory.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Elongation factor Tu
A, B, C, D
392Thermotoga neapolitana (strain ATCC 49049 / DSM 4359 / NS-E)Mutation(s): 0 
Gene Names: tuf
Find proteins for B9K884 (Thermotoga neapolitana (strain ATCC 49049 / DSM 4359 / NS-E))
Go to UniProtKB:  B9K884
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
B, C, D
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B, C, D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.298 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 91.417α = 90.00
b = 173.420β = 90.00
c = 208.178γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
SERGUIdata collection
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-06-19 
  • Released Date: 2018-04-25 
  • Deposition Author(s): Ortlund, E.A.

Funding OrganizationLocationGrant Number
W.M. Keck FoundationUnited States--

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release