1B26

GLUTAMATE DEHYDROGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.225 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of glutamate dehydrogenase from the hyperthermophilic eubacterium Thermotoga maritima at 3.0 A resolution.

Knapp, S.de Vos, W.M.Rice, D.Ladenstein, R.

(1997) J Mol Biol 267: 916-932

  • DOI: https://doi.org/10.1006/jmbi.1996.0900
  • Primary Citation of Related Structures:  
    1B26

  • PubMed Abstract: 

    The extremely thermostable glutamate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima has been crystallized and the three-dimensional structure has been determined by X-ray diffraction methods. Crystals up to a maximum size of 1.2 mm have been grown in 3% polyethylene glycol, 120 mM ammonium acetate and 50 mM bis-tris propane (pH 6.5). The enzyme crystallized in the trigonal space group P3(1)21 with the cell dimensions a = b = 147.3 A, c = 273.6 A. The diffraction limit of these crystals is 3.0 A. Measured diffraction data have a completeness of 94% up to a resolution of 3.0 A and contain 75% of all possible data in the last resolution shell between 3.1 and 3.0 A. The crystal structure of T. maritima glutamate dehydrogenase has been solved by Patterson search methods using the hexameric Pyrococcus furiosus glutamate dehydrogenase as a search model. The crystallographic refinement has been carried out to a maximum resolution of 3.1 A and an crystallographic R-value of 22.5% (Rfree = 29.5%). The three-dimensional structure of the T. maritima enzyme shows typical features of hexameric glutamate dehydrogenases: six subunits are arranged in 32 symmetry. Each subunit consists of two domains connected by a flexible hinge region. Secondary structure elements as well as residues important for the catalytic activity of the enzyme are highly conserved. A structural comparison of the two glutamate dehydrogenases from the hyperthermophiles T. maritima and P. furiosus with the enzyme from the mesophilic bacterium Clostridium symbiosum has revealed that common as well as distinct mechanisms contribute to the thermal stability of these enzymes. The number of intrasubunit ion pairs is increased and the volume of intrasubunit cavities decreased in both thermostable enzymes, whereas striking differences have been observed in the subunit interfaces. In P. furiosus glutamate dehydrogenase the subunit interactions are dominated by ionic interactions realized by large saltbridge networks. However, in T. maritima glutamate dehydrogenase the number of intersubunit ion pairs is reduced and the hydrophobic interactions are increased.


  • Organizational Affiliation

    Karolinska Institutet NOVUM, Centre for Structural Biochemistry (CSB), Huddinge, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUTAMATE DEHYDROGENASE
A, B, C, D, E
A, B, C, D, E, F
416Thermotoga maritimaMutation(s): 0 
EC: 1.4.1.3
UniProt
Find proteins for P96110 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore P96110 
Go to UniProtKB:  P96110
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP96110
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.225 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.13α = 90
b = 147.13β = 90
c = 273.64γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-03
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references