1UXK

Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at the dimer-dimer interface


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Large Improvement in the Thermal Stability of a Tetrameric Malate Dehydrogenase by Single Point Mutations at the Dimer-Dimer Interface.

Bjork, A.Dalhus, B.Mantzilas, D.Sirevag, R.Eijsink, V.G.H.

(2004) J.Mol.Biol. 341: 1215

  • DOI: 10.1016/j.jmb.2004.06.079
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The stability of tetrameric malate dehydrogenase from the green phototrophic bacterium Chloroflexus aurantiacus (CaMDH) is at least in part determined by electrostatic interactions at the dimer-dimer interface. Since previous studies had indicated th ...

    The stability of tetrameric malate dehydrogenase from the green phototrophic bacterium Chloroflexus aurantiacus (CaMDH) is at least in part determined by electrostatic interactions at the dimer-dimer interface. Since previous studies had indicated that the thermal stability of CaMDH becomes lower with increasing pH, attempts were made to increase the stability by removal of (excess) negative charge at the dimer-dimer interface. Mutation of Glu165 to Gln or Lys yielded a dramatic increase in thermal stability at pH 7.5 (+23.6 -- + 23.9 degrees C increase in apparent t(m)) and a more moderate increase at pH 4.4 (+4.6 -- + 5.4 degrees C). The drastically increased stability at neutral pH was achieved without forfeiture of catalytic performance at low temperatures. The crystal structures of the two mutants showed only minor structural changes close to the mutated residues, and indicated that the observed stability effects are solely due to subtle changes in the complex network of electrostatic interactions in the dimer-dimer interface. Both mutations reduced the concentration dependency of thermal stability, suggesting that the oligomeric structure had been reinforced. Interestingly, the two mutations had similar effects on stability, despite the charge difference between the introduced side-chains. Together with the loss of concentration dependency, this may indicate that both E165Q and E165K stabilize CaMDH to such an extent that disruption of the inter-dimer electrostatic network around residue 165 no longer limits kinetic thermal stability.


    Organizational Affiliation

    Department of Molecular Biosciences, University of Oslo, P.O. Box 1041, Blindern, N-0316 Oslo, Norway. alexandra.bjork@bio.uio.no




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MALATE DEHYDROGENASE
A, C
309Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)Mutation(s): 1 
Gene Names: mdh
EC: 1.1.1.37
Find proteins for P80040 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Go to UniProtKB:  P80040
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAD
Query on NAD

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Download CCD File 
A, C
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
CD
Query on CD

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 105.405α = 90.00
b = 105.405β = 90.00
c = 102.305γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-26
    Type: Initial release
  • Version 1.1: 2015-04-15
    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance