4DCS

Crystal Structure of B. subtilis EngA in complex with sulfate ion and GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Potassium Acts as a GTPase-Activating Element on Each Nucleotide-Binding Domain of the Essential Bacillus subtilis EngA.

Foucher, A.E.Reiser, J.B.Ebel, C.Housset, D.Jault, J.M.

(2012) Plos One 7: e46795-e46795

  • DOI: 10.1371/journal.pone.0046795
  • Primary Citation of Related Structures:  4DCT, 4DCU, 4DCV

  • PubMed Abstract: 
  • EngA proteins form a unique family of bacterial GTPases with two GTP-binding domains in tandem, namely GD1 and GD2, followed by a KH (K-homology) domain. They have been shown to interact with the bacterial ribosome and to be involved in its biogenesi ...

    EngA proteins form a unique family of bacterial GTPases with two GTP-binding domains in tandem, namely GD1 and GD2, followed by a KH (K-homology) domain. They have been shown to interact with the bacterial ribosome and to be involved in its biogenesis. Most prokaryotic EngA possess a high GTPase activity in contrast to eukaryotic GTPases that act mainly as molecular switches. Here, we have purified and characterized the GTPase activity of the Bacillus subtilis EngA and two shortened EngA variants that only contain GD1 or GD2-KH. Interestingly, the GTPase activity of GD1 alone is similar to that of the whole EngA, whereas GD2-KH has a 150-fold lower GTPase activity. At physiological concentration, potassium strongly stimulates the GTPase activity of each protein construct. Interestingly, it affects neither the affinities for nucleotides nor the monomeric status of EngA or the GD1 domain. Thus, potassium likely acts as a chemical GTPase-activating element as proposed for another bacterial GTPase like MnmE. However, unlike MnmE, potassium does not promote dimerization of EngA. In addition, we solved two crystal structures of full-length EngA. One of them contained for the first time a GTP-like analogue bound to GD2 while GD1 was free. Surprisingly, its overall fold was similar to a previously solved structure with GDP bound to both sites. Our data indicate that a significant structural change must occur upon K(+) binding to GD2, and a comparison with T. maritima EngA and MnmE structures allowed us to propose a model explaining the chemical basis for the different GTPase activities of GD1 and GD2.


    Organizational Affiliation

    Institut de Biologie Structurale, Université Joseph Fourier Grenoble 1, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTP-BINDING PROTEIN ENGA
A
456Bacillus subtilis (strain 168)Gene Names: der (engA, yphC)
Find proteins for P50743 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P50743
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GDPKd: 8000 nM BINDINGMOAD
GDPKd: 8000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.300α = 90.00
b = 65.790β = 90.00
c = 111.430γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
AMoREphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release