4R98

Chimera of the N-terminal domain of E. coli FeoB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

A GTPase Chimera Illustrates an Uncoupled Nucleotide Affinity and Release Rate, Providing Insight into the Activation Mechanism.

Guilfoyle, A.P.Deshpande, C.N.Font Sadurni, J.Ash, M.R.Tourle, S.Schenk, G.Maher, M.J.Jormakka, M.

(2014) Biophys J 107: L45-L48

  • DOI: 10.1016/j.bpj.2014.10.064
  • Primary Citation of Related Structures:  
    4R98

  • PubMed Abstract: 
  • The release of GDP from GTPases signals the initiation of a GTPase cycle, where the association of GTP triggers conformational changes promoting binding of downstream effector molecules. Studies have implicated the nucleotide-binding G5 loop to be involved in the GDP release mechanism ...

    The release of GDP from GTPases signals the initiation of a GTPase cycle, where the association of GTP triggers conformational changes promoting binding of downstream effector molecules. Studies have implicated the nucleotide-binding G5 loop to be involved in the GDP release mechanism. For example, biophysical studies on both the eukaryotic Gα proteins and the GTPase domain (NFeoB) of prokaryotic FeoB proteins have revealed conformational changes in the G5 loop that accompany nucleotide binding and release. However, it is unclear whether this conformational change in the G5 loop is a prerequisite for GDP release, or, alternatively, the movement is a consequence of release. To gain additional insight into the sequence of events leading to GDP release, we have created a chimeric protein comprised of Escherichia coli NFeoB and the G5 loop from the human Giα1 protein. The protein chimera retains GTPase activity at a similar level to wild-type NFeoB, and structural analyses of the nucleotide-free and GDP-bound proteins show that the G5 loop adopts conformations analogous to that of the human nucleotide-bound Giα1 protein in both states. Interestingly, isothermal titration calorimetry and stopped-flow kinetic analyses reveal uncoupled nucleotide affinity and release rates, supporting a model where G5 loop movement promotes nucleotide release.


    Organizational Affiliation

    Structural Biology Program, Centenary Institute, Sydney, New South Wales, Australia; Faculty of Medicine, Central Clinical School, University of Sydney, Sydney, New South Wales, Australia. Electronic address: m.jormakka@centenary.org.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferrous iron transport protein BA, B271Escherichia coliMutation(s): 0 
Gene Names: feoBb3409JW3372
UniProt
Find proteins for P33650 (Escherichia coli (strain K12))
Explore P33650 
Go to UniProtKB:  P33650
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33650
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNH
Query on GNH

Download Ideal Coordinates CCD File 
C [auth A]AMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H16 N6 O10 P2
ZGPDMUBRWRJAQQ-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.452α = 90
b = 48.452β = 90
c = 233.393γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release