3NEP

1.55A resolution structure of malate dehydrogenase from Salinibacter ruber


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Gradual adaptive changes of a protein facing high salt concentrations.

Coquelle, N.Talon, R.Juers, D.H.Girard, E.Kahn, R.Madern, D.

(2010) J Mol Biol 404: 493-505

  • DOI: 10.1016/j.jmb.2010.09.055
  • Primary Citation of Related Structures:  
    3NEP

  • PubMed Abstract: 
  • Several experimental techniques were applied to unravel fine molecular details of protein adaptation to high salinity. We compared four homologous enzymes, which suggested a new halo-adaptive state in the process of molecular adaptation to high-salt conditions ...

    Several experimental techniques were applied to unravel fine molecular details of protein adaptation to high salinity. We compared four homologous enzymes, which suggested a new halo-adaptive state in the process of molecular adaptation to high-salt conditions. Together with comparative functional studies, the structure of malate dehydrogenase from the eubacterium Salinibacter ruber shows that the enzyme shares characteristics of a halo-adapted archaea-bacterial enzyme and of non-halo-adapted enzymes from other eubacterial species. The S. ruber enzyme is active at the high physiological concentrations of KCl but, unlike typical halo-adapted enzymes, remains folded and active at low salt concentrations. Structural aspects of the protein, including acidic residues at the surface, solvent-exposed hydrophobic surface, and buried hydrophobic surface, place it between the typical halo-adapted and non-halo-adapted proteins. The enzyme lacks inter-subunit ion-binding sites often seen in halo-adapted enzymes. These observations permit us to suggest an evolutionary pathway that is highlighted by subtle trade-offs to achieve an optimal compromise among solubility, stability, and catalytic activity.


    Organizational Affiliation

    IBS, Institut de Biologie Structurale Jean-Pierre Ébel, Extremophilic and Large Molecular Assemblies Team, UMR 5075, CEA, CNRS, Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Malate dehydrogenaseA [auth X]314Salinibacter ruber DSM 13855Mutation(s): 0 
Gene Names: mdhSRU_1571
EC: 1.1.1.37
Find proteins for Q2S289 (Salinibacter ruber (strain DSM 13855 / M31))
Explore Q2S289 
Go to UniProtKB:  Q2S289
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.11α = 90
b = 87.72β = 90
c = 100.45γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance