4CL3

1.70 A resolution structure of the malate dehydrogenase from Chloroflexus aurantiacus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.699 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An Experimental Point of View on Hydration/Solvation in Halophilic Proteins.

Talon, R.Coquelle, N.Madern, D.Girard, E.

(2014) Front.Microbiol. 5: 66

  • DOI: 10.3389/fmicb.2014.00066

  • PubMed Abstract: 
  • Protein-solvent interactions govern the behaviors of proteins isolated from extreme halophiles. In this work, we compared the solvent envelopes of two orthologous tetrameric malate dehydrogenases (MalDHs) from halophilic and non-halophilic bacteria. ...

    Protein-solvent interactions govern the behaviors of proteins isolated from extreme halophiles. In this work, we compared the solvent envelopes of two orthologous tetrameric malate dehydrogenases (MalDHs) from halophilic and non-halophilic bacteria. The crystal structure of the MalDH from the non-halophilic bacterium Chloroflexus aurantiacus (Ca MalDH) solved, de novo, at 1.7 Å resolution exhibits numerous water molecules in its solvation shell. We observed that a large number of these water molecules are arranged in pentagonal polygons in the first hydration shell of Ca MalDH. Some of them are clustered in large networks, which cover non-polar amino acid surface. The crystal structure of MalDH from the extreme halophilic bacterium Salinibacter ruber (Sr) solved at 1.55 Å resolution shows that its surface is strongly enriched in acidic amino acids. The structural comparison of these two models is the first direct observation of the relative impact of acidic surface enrichment on the water structure organization between a halophilic protein and its non-adapted counterpart. The data show that surface acidic amino acids disrupt pentagonal water networks in the hydration shell. These crystallographic observations are discussed with respect to halophilic protein behaviors in solution.


    Related Citations: 
    • The Oligomeric States of Haloarcula Marismortui Malate Dehydrogenase are Modulated by Solvent Components as Shown by Crystallographic and Biochemical Studies.
      Irimia, A.,Ebel, C.,Madern, D.,Richard, S.B.,Cosenza, L.W.,Zaccai, G.,Vellieux, F.M.D.
      (2003) J.Mol.Biol. 326: 859
    • 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
    • Specific Radiation Damage to Acidic Residues and its Relation to Their Chemical and Structural Environment.
      Fioravanti, E.,Vellieux, F.M.D.,Amara, P.,Madern, D.,Weik, M.
      (2007) J.Synchrotron Radia. 14: 84
    • Using Lanthanoid Complexes to Phase Large Macromolecular Assemblies.
      Talon, R.,Kahn, R.,Dura, M.A.,Maury, O.,Vellieux, F.M.D.,Franzetti, B.,Girard, E.
      (2011) J.Synchrotron Radia. 18: 74
    • Sampling the Conformational Energy Landscape of a Hyperthermophilic Protein by Engineering Key Substitutions.
      Colletier, J.,Aleksandrov, A.,Coquelle, N.,Mraihi, S.,Mendoza-Barbera, E.,Field, M.,Madern, D.
      (2012) Mol.Biol.Evol. 29: 1683
    • Gd-Hpdo3A, a Complex to Obtain High-Phasing-Power Heavy-Atom Derivatives for Sad and MAD Experiments: Results with Tetragonal Hen Egg-White Lysozyme.
      Girard, E.,Chantalat, L.,Vicat, J.,Kahn, R.
      (2002) Acta Crystallogr.,Sect.D 58: 1


    Organizational Affiliation

    Institut de Biologie Structurale, Université Grenoble Alpes Grenoble, France ; CEA, DSV, Institut de Biologie Structurale Grenoble, France ; Institut de Biologie Structurale, Centre National de la Recherche Scientifique Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MALATE DEHYDROGENASE
A, D
309Chloroflexus aurantiacus (strain ATCC 29364 / DSM 637 / Y-400-fl)Mutation(s): 0 
Gene Names: mdh
EC: 1.1.1.37
Find proteins for B9LLP6 (Chloroflexus aurantiacus (strain ATCC 29364 / DSM 637 / Y-400-fl))
Go to UniProtKB:  B9LLP6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, D
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.699 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.166 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.226α = 90.00
b = 106.226β = 90.00
c = 102.566γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SHARPphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-03-19
    Type: Database references
  • Version 1.2: 2019-03-06
    Type: Data collection, Experimental preparation, Other