spacer
spacer

PDBsum entry 1gt2

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1gt2
Jmol
Contents
Protein chains
303 a.a. *
Ligands
NAD ×2
Metals
_NA ×6
_CL ×6
Waters ×192
* Residue conservation analysis
Superseded by: 2x0r
PDB id:
1gt2
Name: Oxidoreductase
Title: R207s,r292s mutant of malate dehydrogenase from the halophilic archaeon haloarcula marismortui (holo form)
Structure: Malate dehydrogenase. Chain: a, b. Engineered: yes. Mutation: yes. Other_details: complexed with nadh
Source: Haloarcula marismortui. Organism_taxid: 2238. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.91Å     R-factor:   0.227     R-free:   0.294
Authors: A.Irimia,C.Ebel,F.M.D.Vellieux,S.B.Richard,L.W.Cosenza, G.Zaccai,D.Madern
Key ref:
A.Irimia et al. (2003). The Oligomeric states of Haloarcula marismortui malate dehydrogenase are modulated by solvent components as shown by crystallographic and biochemical studies. J Mol Biol, 326, 859-873. PubMed id: 12581646 DOI: 10.1016/S0022-2836(02)01450-X
Date:
10-Jan-02     Release date:   06-Feb-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q07841  (MDH_HALMA) -  Malate dehydrogenase
Seq:
Struc:
304 a.a.
303 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.37  - Malate dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Citric acid cycle
      Reaction: (S)-malate + NAD+ = oxaloacetate + NADH
(S)-malate
+ NAD(+)
= oxaloacetate
+
NADH
Bound ligand (Het Group name = NAD)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/S0022-2836(02)01450-X J Mol Biol 326:859-873 (2003)
PubMed id: 12581646  
 
 
The Oligomeric states of Haloarcula marismortui malate dehydrogenase are modulated by solvent components as shown by crystallographic and biochemical studies.
A.Irimia, C.Ebel, D.Madern, S.B.Richard, L.W.Cosenza, G.Zaccaï, F.M.Vellieux.
 
  ABSTRACT  
 
The three-dimensional crystal structure of the (R207S, R292S) mutant of malate dehydrogenase from Haloarcula marismortui was solved at 1.95A resolution in order to determine the role of salt bridges and solvent ions in halophilic adaptation and quaternary structure stability. The mutations, located at the dimer-dimer interface, disrupt two inter-dimeric salt bridge clusters that are essential for wild-type tetramer stabilisation. Previous experiments in solution, performed on the double mutant, had shown a tetrameric structure in 4M NaCl, which dissociated into active dimers in 2M NaCl. In order to establish if the active dimeric form is a product of the mutation, or if it also exists in the wild-type protein, complementary studies were performed on the wild-type enzyme by analytical centrifugation and small angle neutron scattering experiments. They showed the existence of active dimers in NaF, KF, Na(2)SO(4), even in the absence of NADH, and in the presence of NADH at concentrations of NaCl below 0.3M. The crystal structure shows a tetramer that, in the absence of the salt bridge clusters, appears to be stabilized by a network of ordered water molecules and by Cl(-) binding at the dimer-dimer interface. The double mutant and wild-type dimer folds are essentially identical (the r.m.s. deviation between equivalent C(alpha) positions is 0.39A). Chloride ions are also observed at the monomer-monomer interfaces of the mutant, contributing to the stability of each dimer against low salt dissociation. Our results support the hypothesis that extensive binding of water and salt is an important feature of adaptation to a halophilic environment.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Quaternary structure of (R207S, R292S) Hm MalDH and ion binding to the interface. The quaternary structure of (R207S, R292S) MalDH is a tetrameric complex. The structure is shown in two orthogonal views. The monomers are labelled A to D. Secondary structures are shown as thick ribbons. The NADH cofactor, displayed in green, is bound to the catalytic site of each monomer. Chloride ions, rendered as yellow spheres, are localised at subunit interfaces. The water molecules (small red spheres) form networks on the external surface and at internal interfaces between dimers. The two tight AB and CD dimeric assemblies delimit an elongated cavity at their interface. The regions where the protein–protein interactions across the A–D interface remain after the salt bridges were disrupted by the arginine to serine mutations are highlighted in cyan. The Figure was generated using Molscript,[63] Bobscript, [64] and Raster3D. [65]
Figure 3.
Figure 3. Changes in salt bridge clusters and chloride ion binding at the interfaces. Highlights of the specific interactions occurring at the interfaces. The amino acids involved in three areas of interaction between monomers are shown as ball-and-stick. The labels of the mutated residues are underlined. Chloride ions are shown as large yellow spheres, water molecules are represented by small red spheres, and the broken lines indicate the interactions between opposite charges. (a) The modifications of the previously described cluster 3[22] are presented for the AD monomer-monomer interface. The extended protein-protein salt bridges at the dimer-dimer interface, present in wild-type MalDH, are replaced in the double mutant by four water molecules. New positions of the Glu188A and Glu188D side-chains in the double mutant (displayed in thin orange ball-and-stick) are presented in comparison with their initial positions in wild-type (shown in thin grey). Two chloride ions (Cl -1001A and Cl -1002D) are bound in equivalent positions at the two extremities of this cluster. These chlorides correspond to Cl -1003B and Cl -1004C, which connect the monomers B and C at the opposite end of the molecule. (b) After the R292S mutation, the complex salt bridges forming the previously described "cluster 2"[22] are disrupted. There is a single interaction, connecting the side-chain of Asn186 to that of Gly266, which remains in this cluster. (c) Two chloride ions (Cl -1007C and Cl -1008D) are located close to the tight C-D monomer-monomer interface, where their interactions with the neighbouring residues are almost identical. These negatively charged ions are surrounded by positive charges, mainly the side-chains of arginine residues. Arginine 43C is modelled by two alternate conformations. The distances between the chloride ions and surrounding amino acids are shown. The area described in this Figure is equivalent to the corresponding area at the AB interface.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 326, 859-873) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19184366 A.Pradhan, P.Mukherjee, A.K.Tripathi, M.A.Avery, L.A.Walker, and B.L.Tekwani (2009).
Analysis of quaternary structure of a [LDH-like] malate dehydrogenase of Plasmodium falciparum with oligomeric mutants.
  Mol Cell Biochem, 325, 141-148.  
18189118 Y.Cao, L.Liao, X.W.Xu, A.Oren, C.Wang, X.F.Zhu, and M.Wu (2008).
Characterization of alcohol dehydrogenase from the haloalkaliphilic archaeon Natronomonas pharaonis.
  Extremophiles, 12, 471-476.  
17406782 A.K.Bandyopadhyay, G.Krishnamoorthy, L.C.Padhy, and H.M.Sonawat (2007).
Kinetics of salt-dependent unfolding of [2Fe-2S] ferredoxin of Halobacterium salinarum.
  Extremophiles, 11, 615-625.  
17215355 M.Tehei, B.Franzetti, K.Wood, F.Gabel, E.Fabiani, M.Jasnin, M.Zamponi, D.Oesterhelt, G.Zaccai, M.Ginzburg, and B.Z.Ginzburg (2007).
Neutron scattering reveals extremely slow cell water in a Dead Sea organism.
  Proc Natl Acad Sci U S A, 104, 766-771.  
17018059 S.Franceschini, P.Ceci, F.Alaleona, E.Chiancone, and A.Ilari (2006).
Antioxidant Dps protein from the thermophilic cyanobacterium Thermosynechococcus elongatus.
  FEBS J, 273, 4913-4928.
PDB code: 2c41
15856483 F.Rodier, R.P.Bahadur, P.Chakrabarti, and J.Janin (2005).
Hydration of protein-protein interfaces.
  Proteins, 60, 36-45.  
15894606 L.Premkumar, H.M.Greenblatt, U.K.Bageshwar, T.Savchenko, I.Gokhman, J.L.Sussman, and A.Zamir (2005).
Three-dimensional structure of a halotolerant algal carbonic anhydrase predicts halotolerance of a mammalian homolog.
  Proc Natl Acad Sci U S A, 102, 7493-7498.
PDB code: 1y7w
15014443 A.Irimia, D.Madern, G.Zaccaï, and F.M.Vellieux (2004).
Methanoarchaeal sulfolactate dehydrogenase: prototype of a new family of NADH-dependent enzymes.
  EMBO J, 23, 1234-1244.
PDB codes: 1rfm 2x06
15317584 A.K.Tripathi, P.V.Desai, A.Pradhan, S.I.Khan, M.A.Avery, L.A.Walker, and B.L.Tekwani (2004).
An alpha-proteobacterial type malate dehydrogenase may complement LDH function in Plasmodium falciparum. Cloning and biochemical characterization of the enzyme.
  Eur J Biochem, 271, 3488-3502.  
15221656 D.Madern, M.Camacho, A.Rodríguez-Arnedo, M.J.Bonete, and G.Zaccai (2004).
Salt-dependent studies of NADP-dependent isocitrate dehydrogenase from the halophilic archaeon Haloferax volcanii.
  Extremophiles, 8, 377-384.  
15306381 G.Zaccai (2004).
The effect of water on protein dynamics.
  Philos Trans R Soc Lond B Biol Sci, 359, 1269.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.