1CER

DETERMINANTS OF ENZYME THERMOSTABILITY OBSERVED IN THE MOLECULAR STRUCTURE OF THERMUS AQUATICUS D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 2.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

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This is version 1.2 of the entry. See complete history


Literature

Determinants of enzyme thermostability observed in the molecular structure of Thermus aquaticus D-glyceraldehyde-3-phosphate dehydrogenase at 25 Angstroms Resolution.

Tanner, J.J.Hecht, R.M.Krause, K.L.

(1996) Biochemistry 35: 2597-2609

  • DOI: 10.1021/bi951988q
  • Primary Citation of Related Structures:  
    1CER

  • PubMed Abstract: 
  • The crystal structure of holo D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the extreme thermophile Thermus aquaticus has been solved at 2.5 Angstroms resolution. To study the determinants of thermostability, we compare our structure to four other GAPDHs ...

    The crystal structure of holo D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the extreme thermophile Thermus aquaticus has been solved at 2.5 Angstroms resolution. To study the determinants of thermostability, we compare our structure to four other GAPDHs. Salt links, hydrogen bonds, buried surface area, packing density, surface to volume ratio, and stabilization of alpha-helices and beta-turns are analyzed. We find a strong correlation between thermostability and the number of hydrogen bonds between charged side chains and neutral partners. These charged-neutral hydrogen bonds provide electrostatic stabilization without the heavy desolvation penalty of salt links. The stability of thermophilic GAPDHs is also correlated with the number of intrasubunit salt links and total hydrogen bonds. Charged residues, therefore, play a dual role in stabilization by participating not only in salt links but also in hydrogen bonds with a neutral partner. Hydrophobic effects allow for discrimination between thermophiles and psychrophiles, but not within the GAPDH thermophiles. There is, however, an association between thermostability and decreasing enzyme surface to volume ratio. Finally, we describe several interactions present in both our GAPDH and a hyperthermophilic GAPDH that are absent in the less thermostable GAPDHs. These include a four-residue salt link network, a hydrogen bond near the active site, an intersubunit salt link, and several buried Ile residues.


    Related Citations: 
    • Preliminary Crystallographic Analysis of Glyceraldehyde-3-Phosphate Dehydrogenase from the Extreme Thermophile Thermus Aquaticus
      Tanner, J., Hecht, R.M., Pisegna, M., Seth, D.M., Krause, K.L.
      (1994) Acta Crystallogr D Biol Crystallogr 50: 744

    Organizational Affiliation

    Department of Biochemical and Biohysical Sciences, University of Houston, Houston, Texas 77204-5934, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASEE [auth A], F [auth B], G [auth C], H [auth D], A [auth O], B [auth P], C [auth Q], D [auth R]331Thermus aquaticusMutation(s): 0 
Gene Names: THERMUS AQUATICUS GAPDHgap
EC: 1.2.1.12
UniProt
Find proteins for P00361 (Thermus aquaticus)
Explore P00361 
Go to UniProtKB:  P00361
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.77α = 90
b = 148.77β = 90
c = 149.5γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance