3NEP

1.55A resolution structure of malate dehydrogenase from Salinibacter ruber


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.551 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.168 

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
  • Also Cited By: 4BGT, 4BGU, 4BGV, 4CL3

  • 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 ...

    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 √Čbel, Extremophilic and Large Molecular Assemblies Team, UMR 5075, CEA, CNRS, Universit√© Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Malate dehydrogenase
X
314Salinibacter ruber (strain DSM 13855 / M31)Gene Names: mdh
EC: 1.1.1.37
Find proteins for Q2S289 (Salinibacter ruber (strain DSM 13855 / M31))
Go to UniProtKB:  Q2S289
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.551 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.168 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 76.110α = 90.00
b = 87.720β = 90.00
c = 100.450γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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