1D3A | pdb_00001d3a

CRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 
    0.244 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.198 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1D3A

This is version 1.4 of the entry. See complete history

Literature

Halophilic adaptation: novel solvent protein interactions observed in the 2.9 and 2.6 A resolution structures of the wild type and a mutant of malate dehydrogenase from Haloarcula marismortui.

Richard, S.B.Madern, D.Garcin, E.Zaccai, G.

(2000) Biochemistry 39: 992-1000

  • DOI: https://doi.org/10.1021/bi991001a
  • Primary Citation Related Structures: 
    1D3A, 2HLP

  • PubMed Abstract: 

    Previous biophysical studies of tetrameric malate dehydrogenase from the halophilic archaeon Haloarcula marismortui (Hm MalDH) have revealed the importance of protein-solvent interactions for its adaptation to molar salt conditions that strongly affect protein solubility, stability, and activity, in general. The structures of the E267R stability mutant of apo (-NADH) Hm MalDH determined to 2.6 A resolution and of apo (-NADH) wild type Hm MalDH determined to 2.9 A resolution, presented here, highlight a variety of novel protein-solvent features involved in halophilic adaptation. The tetramer appears to be stabilized by ordered water molecule networks and intersubunit complex salt bridges "locked" in by bound solvent chloride and sodium ions. The E267R mutation points into a central ordered water cavity, disrupting protein-solvent interactions. The analysis of the crystal structures showed that halophilic adaptation is not aimed uniquely at "protecting" the enzyme from the extreme salt conditions, as may have been expected, but, on the contrary, consists of mechanisms that harness the high ionic concentration in the environment.


  • Organizational Affiliation
    • Institut de Biologie Structurale, CEA-CNRS, 41 Avenue des Martyrs, F-38027 Grenoble Cedex 1, France.

Macromolecule Content 

  • Total Structure Weight: 65.51 kDa 
  • Atom Count: 4,637 
  • Modeled Residue Count: 606 
  • Deposited Residue Count: 606 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HALOPHILIC MALATE DEHYDROGENASE
A, B
303Haloarcula marismortuiMutation(s): 0 
EC: 1.1.1.37
UniProt
Find proteins for Q07841 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore Q07841 
Go to UniProtKB:  Q07841
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07841
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free:  0.244 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.198 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.78α = 90
b = 131.33β = 90
c = 125.45γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2014-04-09
    Changes: Database references
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations