1TRK

REFINED STRUCTURE OF TRANSKETOLASE FROM SACCHAROMYCES CEREVISIAE AT 2.0 ANGSTROMS RESOLUTION

Summary for 1TRK

• Entry DOI: 10.2210/pdb1trk/pdb
• Descriptor: TRANSKETOLASE, CALCIUM ION, THIAMINE DIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: transferase(ketone residues)
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Total number of polymer chains: 2
• Total formula weight: 148705.57

Authors

Lindqvist, Y.,Schneider, G.,Nikkola, M. (deposition date: 1993-11-22, release date: 1994-04-30, Last modification date: 2024-02-14)

Primary citation

Nikkola, M.,Lindqvist, Y.,Schneider, G.
Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 A resolution.
J.Mol.Biol., 238:387-404, 1994

PubMed Abstract: The crystal structure of transketolase from Saccharomyces cerevisiae has been refined to a crystallographic residual of 15.7% at 2.0 A resolution using the program package X-PLOR. The refined model of the transketolase homodimer, corresponding to 1356 amino acid residues in the asymmetric unit, consists of 10,396 protein atoms, 1040 solvent molecules, 52 thiamine diphosphate atoms and two calcium ions. All amino acid residues except for the two N-terminal residues of the two subunits are defined in the electron density maps and refined. The estimated root-mean-square (r.m.s.) error of the model is less than 0.2 A as deduced from Luzzati plots. The r.m.s. deviation from ideality is 0.017 A for bond distances and 3.1 degrees for bond angles. The main-chain torsion angles of non-glycine residues lie within the allowed regions of the Ramachandran plots. The model shows a very good fit to the electron density maps. The average B-factor for all protein atoms in the first subunit is 19 A2, and 15A2 in the second. The average B-factor for solvent atoms is 32A2. The two subunits of transketolase were refined independently and have nearly identical structures with an r.m.s. deviation of 0.24 A for C alpha atoms 3 to 680, and slightly less when aligning the individual domains. A few exceptions from the 2-fold symmetry are found, mostly in the surface residues. The thiamine diphosphate cofactors have identical conformations. The cofactor is shielded from solvent except for the C-2 atom of the thiazolium ring. A calcium ion is bound to the diphosphate group of thiamine and protein ligands. The metal binding site and the interactions of thiamine diphosphate with protein residues are described. A network of hydrogen bonds consisting of glutamic acid residues and internal water molecules connects the two thiamine diphosphate molecules. Its structure and possible functional implications are discussed.

PubMed: 8176731
DOI: 10.1006/jmbi.1994.1299

Experimental method

X-RAY DIFFRACTION (2 Å)