1BVU

GLUTAMATE DEHYDROGENASE FROM THERMOCOCCUS LITORALIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure determination of the glutamate dehydrogenase from the hyperthermophile Thermococcus litoralis and its comparison with that from Pyrococcus furiosus

Britton, K.L.Yip, K.S.Sedelnikova, S.E.Stillman, T.J.Adams, M.W.Ma, K.Maeder, D.L.Robb, F.T.Tolliday, N.Vetriani, C.Rice, D.W.Baker, P.J.

(1999) J.Mol.Biol. 293: 1121-1132

  • DOI: 10.1006/jmbi.1999.3205

  • PubMed Abstract: 
  • Glutamate dehydrogenase catalyses the oxidative deamination of glutamate to 2-oxoglutarate with concomitant reduction of NAD(P)(+), and has been shown to be widely distributed in nature across species ranging from psychrophiles to hyperthermophiles. ...

    Glutamate dehydrogenase catalyses the oxidative deamination of glutamate to 2-oxoglutarate with concomitant reduction of NAD(P)(+), and has been shown to be widely distributed in nature across species ranging from psychrophiles to hyperthermophiles. Extensive characterisation of this enzyme isolated from hyperthermophilic organisms has led to its adoption as a model system for analysing the determinants of thermal stability. The crystal structure of the extremely thermostable glutamate dehydrogenase from Thermococcus litoralis has been determined at 2.5 A resolution, and has been compared to that from the hyperthermophile Pyrococcus furiosus. The two enzymes are 87 % identical in sequence, yet differ 16-fold in their half-lives at 104 degrees C. This is the first reported comparative analysis of the structures of a multisubunit enzyme from two closely related yet distinct hyperthermophilies. The less stable T. litoralis enzyme has a decreased number of ion pair interactions; modified patterns of hydrogen bonding resulting from isosteric sequence changes; substitutions that decrease packing efficiency; and substitutions which give rise to subtle but distinct shifts in both main-chain and side-chain elements of the structure. This analysis provides a rational basis to test ideas on the factors that confer thermal stability in proteins through a combination of mutagenesis, calorimetry, and structural studies.


    Related Citations: 
    • Crystallisation of the Glutamate Dehydrogenase from the Hyperthermophilic Archaeon Thermococcus Litoralis
      Sedelnikova, S.E.,Yip, K.S.-P.,Stillman, T.J.,Ma, K.,Adams, M.W.W.,Robb, F.T.,Rice, D.W.
      (1996) Acta Crystallogr.,Sect.D 52: 1185
    • Protein Thermostability Above 100C: A Key Role for Ionic Interactions
      Vetriani, C.,Maeder, D.L.,Tolliday, N.,Yip, K.S.-P.,Stillman, T.J.,Britton, K.L.,Rice, D.W.,Klump, H.H.,Robb, F.T.
      (1998) Proc.Natl.Acad.Sci.USA 95: 12300


    Organizational Affiliation

    University of Sheffield, Sheffield, S10 2TN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (GLUTAMATE DEHYDROGENASE)
A, B, C, D, E, F
418Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C)Gene Names: gdhA
EC: 1.4.1.3
Find proteins for Q56304 (Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C))
Go to UniProtKB:  Q56304
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 141.900α = 90.00
b = 197.500β = 113.60
c = 125.700γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
TNTrefinement
CCP4data scaling
ROTAVATAdata reduction
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance