Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 Å resolution

doi:10.1016/0022-2836(87)90635-8

Journal of Molecular Biology

Volume 193, Issue 1, 5 January 1987, Pages 171-187

https://doi.org/10.1016/0022-2836(87)90635-8 Get rights and content

Abstract

The structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus has been crystallographically refined at 1.8 Å resolution using restrained least-squares refinement methods. The final crystallographic R-factor for 93,120 reflexions with F > 3σ(F) is 0.177. The asymmetric unit of the crystal contains a complete tetramer, the final model of which incorporates a total of 10,272 unique protein and coenzyme atoms together with 677 bound solvent molecules. The structure has been analysed with respect to molecular symmetry, intersubunit contacts, coenzyme binding and active site geometry. The refined model shows the four independent subunits to be remarkably similar apart from local deviations due to intermolecular contacts within the crystal lattice.

A number of features are revealed that had previously been misinterpreted from an earlier 2.7 Å electron density map. Arginine at position 195 (previously thought to be a glycine) contributes to the formation of the anion binding sites in the active site pocket, which are involved in binding of the substrate and inorganic phosphates during catalysis. This residue seems to be structurally equivalent to the conserved Argl94 in the enzyme from other sources. In the crystal both of the anion binding sites are occupied by sulphate ions. The ND atom of the catalytically important His176 is hydrogen-bonded to the mainchain carbonyl oxygen of Ser177, thus fixing the plane of the histidine imidazole ring and preventing rotation.

The analysis has revealed the presence of several internal salt-bridges stabilizing the tertiary and quaternary structure. A significant number of buried water molecules have been found that play an important role in the structural integrity of the molecule.

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^☆: The research was funded by the Medical Research Council of Great Britain. P.C.E.M. was the holder of an SERC studentship.

^†: On leave from the University of Lódź, Poland.

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Journal of Molecular Biology

Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 Å resolution☆

Abstract

J. Mol. Biol

J. Biol. Chem

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Biol. Chem

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Biol. Chem

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Biol. Chem

Acta Crystallogr. sect. A

Nature (London)

Eur. J. Biochem