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PDBsum entry 1trk
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Transferase(ketone residues)
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PDB id
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1trk
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Refined structure of transketolase from saccharomyces cerevisiae at 2.0 a resolution.
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Authors
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M.Nikkola,
Y.Lindqvist,
G.Schneider.
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Ref.
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J Mol Biol, 1994,
238,
387-404.
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
93%.
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Abstract
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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.
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Secondary reference #1
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Title
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Yeast tkl1 gene encodes a transketolase that is required for efficient glycolysis and biosynthesis of aromatic amino acids.
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Authors
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M.Sundström,
Y.Lindqvist,
G.Schneider,
U.Hellman,
H.Ronne.
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Ref.
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J Biol Chem, 1993,
268,
24346-24352.
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PubMed id
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Secondary reference #2
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Title
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Three-Dimensional structure of transketolase, A thiamine diphosphate dependent enzyme, At 2.5 a resolution.
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Authors
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Y.Lindqvist,
G.Schneider,
U.Ermler,
M.Sundström.
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Ref.
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Embo J, 1992,
11,
2373-2379.
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PubMed id
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Secondary reference #3
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Title
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Preliminary crystallographic data for transketolase from yeast.
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Authors
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G.Schneider,
M.Sundström,
Y.Lindqvist.
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Ref.
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J Biol Chem, 1989,
264,
21619-21620.
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PubMed id
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