4CL3

1.70 A resolution structure of the malate dehydrogenase from Chloroflexus aurantiacus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

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
  • Primary Citation of Related Structures:  
    4CL3

  • 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: 
    • 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
    • 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 Radiat 14: 84
    • 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
    • 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 D Biol Crystallogr 58: 1
    • 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 Radiat 18: 74

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MALATE DEHYDROGENASEAD309Chloroflexus aurantiacus Y-400-flMutation(s): 0 
Gene Names: mdhChy400_0980
EC: 1.1.1.37
Find proteins for B9LLP6 (Chloroflexus aurantiacus (strain ATCC 29364 / DSM 637 / Y-400-fl))
Explore B9LLP6 
Go to UniProtKB:  B9LLP6
Protein Feature View
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 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download CCD File 
A, D
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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

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

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.226α = 90
b = 106.226β = 90
c = 102.566γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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